From owner-chemistry@ccl.net Mon Dec 8 10:50:01 2014 From: "conor douglas parks coparks2012|-|gmail.com" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50800-141208104854-10549-aEQT7Mdxi8V9hQKuZ/xdrg[-]server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 8 Dec 2014 10:48:53 -0500 Sent to CCL by: "conor douglas parks" [coparks2012{}gmail.com] Hello, thank you for your response. I am planning on using lammps. Thus, I need to dive into the literature and find the parameters myself. However that being said, is there a way that you know of to have gromacs output the parameters for me? I originally was going to use charmm. However, I could not find a complete parameter set to look through. I found the OPLs parameters very quickly. Do you know where I can go to find the complete charmm parameter set? conor > "Elvis Martis elvis_bcp- -elvismartis.in" wrote: > > Sent to CCL by: Elvis Martis [elvis_bcp^-^elvismartis.in] > --_D70DBD85-A969-42B9-A9C8-FFDADF20AB06_ > Content-Transfer-Encoding: quoted-printable > Content-Type: text/plain; charset="utf-8" > > Hello > Which program do you intend to perform your simulation? > I can help you with amber parameters. If you using Desmond then, there shou= > ldn't be any problem. And for gromacs there are web servers and scripts fo= > r this purpose. > > > -----Original Message----- > > From: "conor douglas parks coparks2012=3Dgmail.com" t> > Sent: =E2=80=8E08-=E2=80=8E12-=E2=80=8E2014 06:18 > To: "Martis, Elvis Martis " > Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid > > > Sent to CCL by: "conor douglas parks" [coparks2012.]|[.gmail.com] > Hello, I am in the process of performing my first molecular dynamics simula= > tions for an actual research=20 > project, and have some questions regarding the choice of the appropriate fo= > rce field parameters from=20 > the OPLS parameter set. My molecule is Tetrolic acid, and has what I believ= > e are the following atom=20 > types > > > atom# atom type atom symbol description > 209 3 C carboxylic acid C= > OOH > 210 4 O carboxylic acid C= > =3DO > 211 5 OH carboxylic acid -O= > H > 212 7 HO carboxylic acid -C= > OOH > 769 19 CZ alkyne RCCR > 80 13 CT Alkane CH3 > 85 46 HC alkane H-C > > Now from what I can tell, I believe the following angles need to be specifi= > ed for Tetrolic acid > > 4 3 5 =20 > 3 5 7 > 4 3 19 > 13 19 19 > 19 19 3 > 19 13 46 > > I can not find any parameters for the angle bending for the 19-19-3 angle i= > n the OPLS parameter set=20 > (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone h= > ave any suggestions of=20 > how I could obtain a suitable parameter for this type of interaction? > > Similary for the torsion, I believe I need parameters for > > 4 3 5 7 > 7 5 3 19 > 4 3 19 19 > 46 13 19 19 > > However, I cannot find any parameters for the 46 13 19 19 group or the 4 3 = > 19 19. Similarly, are there=20 > any suggestions for what I can do here? Are there any issues with the atom = > types I have selected for=20 > tetrolic acid? The two triple bonded C have given me some concern. > > > > -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi- bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--_D70DBD85-A969-42B9-A9C8- FFDADF20AB06_ > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; charset="utf-8" > > =3Dutf-8">
font-size: 11pt;">Hello
Which program do you intend to perform your simu= > lation?
I can help you with amber parameters. If you using Desmond then,= > there shouldn't be any problem. And  for gromacs there are web server= > s and scripts for this purpose.
tyle=3D"font-family: Calibri,sans-serif; font-size: 11pt; font-weight: bold= > ;">From: 11pt;">conor douglas parks copar= > ks2012=3Dgmail.com
erif; font-size: 11pt; font-weight: bold;">Sent: -family: Calibri,sans-serif; font-size: 11pt;">=E2=80=8E08-=E2=80=8E12-=E2= > =80=8E2014 06:18
font-size: 11pt; font-weight: bold;">To: Calibri,sans-serif; font-size: 11pt;"> tis.in">Martis, Elvis Martis
ily: Calibri,sans-serif; font-size: 11pt; font-weight: bold;">Subject: an>CCL: C= > hoosing appropriate OPLS parameters for Tetrolic Acid

<= > br>Sent to CCL by: "conor douglas parks" [coparks2012.]|[.gmail.com]
Hello= > , I am in the process of performing my first molecular dynamics simulations= > for an actual research
project, and have some questions regarding the = > choice of the appropriate force field parameters from
the OPLS paramete= > r set. My molecule is Tetrolic acid, and has what I believe are the followi= > ng atom
types


atom#     atom type &= > nbsp;     atom symbol      des= > cription
209          3&nbs= > p;            &= > nbsp;            C&n= > bsp;            = > ;    carboxylic acid COOH
210    &nbs= > p;     4        = > ;            &n= > bsp;     O       &nb= > sp;         carboxylic acid C=3DO r>211          5  &n= > bsp;            = > ;           OH  = > ;             c= > arboxylic acid -OH
212        &n= > bsp; 7           &nb= > sp;            = >   HO           = >     carboxylic acid -COOH
769    &nbs= > p;     19       &nbs= > p;            &= > nbsp;   CZ         &= > nbsp;     alkyne RCCR
80    &nbs= > p;       13     &nbs= > p;            &= > nbsp;     CT       &= > nbsp;       Alkane CH3
85   = > ;         46    = > ;            &n= > bsp;       HC     &n= > bsp;         alkane H-C

Now = > > from what I can tell, I believe the following angles need to be specified f= > or Tetrolic acid

4    3     = > 5    
3    5    = > ;  7
4    3     19
13 &n= > bsp; 19  19
19   19   3
19   13&nb= > sp;  46

I can not find any parameters for the angle bending for= > the 19-19-3 angle in the OPLS parameter set
(http://dasher.wustl.edu/f= > fe/distribution/params/oplsaa.prm). Does anyone have any suggestions of >how I could obtain a suitable parameter for this type of interaction?
<= > br>Similary for the torsion, I believe I need parameters for

4 3 5 7= >
7 5 3 19
4 3 19 19
46 13 19 19

However, I cannot find any = > parameters for the 46 13 19 19 group or the 4 3 19 19. Similarly, are there= >
any suggestions for what I can do here? Are there any issues with the = > atom types I have selected for
tetrolic acid? The two triple bonded C h= > ave given me some concern.



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= > > --_D70DBD85-A969-42B9-A9C8-FFDADF20AB06_-- > > From owner-chemistry@ccl.net Mon Dec 8 11:24:01 2014 From: "conor douglas parks coparks2012|gmail.com" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50801-141208105145-11647-60REzAKj9wv0veQ3AQGu0A(!)server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 8 Dec 2014 10:51:44 -0500 Sent to CCL by: "conor douglas parks" [coparks2012*o*gmail.com] Hey simon, thank you for your response. I actually have read that paper already. Unfortunately, jie just says she uses OPLS and CHARMM without actually providing the parameters she used. I was hoping to avoid the issue of having to use a mixed force field by just using OPLS, but it looks like I might have to resort to charmm-opls. Do you know where I can go to find the charmm parameters for this type of molecule? > "Simon Halstead joyjoyhappyjoy-,-yahoo.co.uk" wrote: > > Sent to CCL by: Simon Halstead [joyjoyhappyjoy:-:yahoo.co.uk] > ------=_Part_6882799_1229177045.1418005247965 > Content-Type: text/plain; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > > Hi, > the choice of atoms looks reasonable - a quick way to check would be to mak= > e sure all the charges sum to zero.The problem you have is that OPLS doesn'= > t include every possible combination of functional groups - an alkyne to ca= > rboxylic acid is perhaps not very common. You have a few choices about what= > to do. > First, you could constrain part of the molecule which is a good choice if t= > he structure of that area is not likely to fluctuate much.Second, you could= > look for additional parameters in the literature. There are many papers pr= > oviding additional or improved OPLS parameters. For example, The Journal of= > Physical Chemistry B - Computational Study of Solvent Effects on the Molec= > ular Self-Assembly of Tetrolic Acid in Solution and Implications for the Po= > lymorph Formed from Crystallization (ACS Publications) provides some parame= > ters you could use (though this is a mixture of CHARMM and OPLS).Finally, y= > ou could calculate extra parameters yourself using some higher levels of th= > eory. > > Good luck, > Simon > From: conor douglas parks coparks2012=3Dgmail.com l.net> > To: "Halstead, Simon " =20 > Sent: Monday, December 8, 2014 7:10 AM > Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid > =20 > > Sent to CCL by: "conor douglas parks" [coparks2012.{=}.gmail.com] > Hello, I am in the process of performing my first molecular dynamics simula= > tions for an actual research=20 > project, and have some questions regarding the choice of the appropriate fo= > rce field parameters from=20 > the OPLS parameter set. My molecule is Tetrolic acid, and has what I believ= > e are the following atom=20 > types > > > atom#=C2=A0 =C2=A0 atom type=C2=A0 =C2=A0 =C2=A0 atom symbol=C2=A0 =C2=A0 = > =C2=A0 description > 209=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid COOH > 210=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 O=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid C=3DO > 211=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 OH=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid -OH > 212=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HO=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid -COOH > 769=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 19=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CZ=C2=A0 =C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 alkyne RCCR > 80=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 13=C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CT=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Alkane CH3 > 85=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 46=C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HC=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 alkane H-C > > Now from what I can tell, I believe the following angles need to be specifi= > ed for Tetrolic acid > > 4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0=20 > 3=C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 7 > 4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 19 > 13=C2=A0 19=C2=A0 19 > 19=C2=A0 19=C2=A0 3 > 19=C2=A0 13=C2=A0 46 > > I can not find any parameters for the angle bending for the 19-19-3 angle i= > n the OPLS parameter set=20 > (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone h= > ave any suggestions of=20 > how I could obtain a suitable parameter for this type of interaction? > > Similary for the torsion, I believe I need parameters for > > 4 3 5 7 > 7 5 3 19 > 4 3 19 19 > 46 13 19 19 > > However, I cannot find any parameters for the 46 13 19 19 group or the 4 3 = > 19 19. Similarly, are there=20 > any suggestions for what I can do here? Are there any issues with the atom = > types I have selected for=20 > tetrolic acid? The two triple bonded C have given me some concern. > > > > -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 > =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------ =_Part_6882799_1229177045.1418005247965 > Content-Type: text/html; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > >
lveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;fo= > nt-size:14px">
Hi,
=3D"yui_3_16_0_1_1418003648379_3261">
003648379_3262" dir=3D"ltr">the choice of atoms looks reasonable - a quick = > way to check would be to make sure all the charges sum to zero.
d=3D"yui_3_16_0_1_1418003648379_3263" dir=3D"ltr">The problem you have is t= > hat OPLS doesn't include every possible combination of functional groups - = > an alkyne to carboxylic acid is perhaps not very common. You have a few cho= > ices about what to do.
=3D"ltr">
= > First, you could constrain part of the molecule which is a good choice if t= > he structure of that area is not likely to fluctuate much.
yui_3_16_0_1_1418003648379_3243" dir=3D"ltr">Second, you could look for add= > itional parameters in the literature. There are many papers providing addit= > ional or improved OPLS parameters. For example, 03648379_3242" href=3D"http://pubs.acs.org/doi/pdf/10.1021/jp7106582">The J= > ournal of Physical Chemistry B - Computational Study of Solvent Effects on = > the Molecular Self-Assembly of Tetrolic Acid in Solution and Implications f= > or the Polymorph Formed from Crystallization (ACS Publications) provide= > s some parameters you could use (though this is a mixture of CHARMM and OPL= > S).
Finally, y= > ou could calculate extra parameters yourself using some higher levels of th= > eory.

>
Good l= > uck,

<= > span>Simon

yle=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida= > Grande, sans-serif; font-size: 14px;">
79_3794" style=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Ar= > ial, Lucida Grande, sans-serif; font-size: 16px;">
1418003648379_3793" dir=3D"ltr">
1418003648379_5747" face=3D"Arial" size=3D"2"> t:bold;">From: conor douglas parks coparks2012=3Dgmail.com <o= > wner-chemistry{=}ccl.net>
To: pan> "Halstead, Simon " <joyjoyhappyjoy{=}yahoo.co.uk>
= > Sent: Monday, December 8,= > 2014 7:10 AM
Subject:= > CCL: Choosing appropriate OPLS parameters for Tetrolic Acid
 div>


Sent to CCL by: "conor douglas = > parks" [ s2012.{=}.gmail.com">coparks2012.{=}.gmail.com]
Hello, I am in the proce= > ss of performing my first molecular dynamics simulations for an actual rese= > arch
project, and have some questions regarding the choice of the appro= > priate force field parameters from
the OPLS parameter set. My molecule = > is Tetrolic acid, and has what I believe are the following atom
types r>

atom#    atom type      atom symbol&nb= > sp;     description
209          3&nb= > sp;                     &= > nbsp;   C                carb= > oxylic acid COOH
210          4    &n= > bsp;                     = > O                carboxylic acid C= > =3DO
211          5        = >                   OH  &nb= > sp;           carboxylic acid -OH
212  &n= > bsp;       7             = >             HO        &n= > bsp;     carboxylic acid -COOH
769       = >   19                  &n= > bsp;     CZ              alky= > ne RCCR
80            13    &nbs= > p;                   CT  = >             Alkane CH3
85    &n= > bsp;       46             = > ;           HC          &= > nbsp;   alkane H-C

Now from what I can tell, I believe the fol= > lowing angles need to be specified for Tetrolic acid

4    = > 3      5   
3    5    &nb= > sp; 7
4    3    19
13  19  19
19&n= > bsp; 19  3
19  13  46

I can not find any param= > eters for the angle bending for the 19-19-3 angle in the OPLS parameter set= >
( " target=3D"_blank">http://dasher.wustl.edu/ffe/distribution/params/oplsaa.= > prm). Does anyone have any suggestions of
how I could obtain a suit= > able parameter for this type of interaction?

Similary for the torsio= > n, I believe I need parameters for

4 3 5 7
7 5 3 19
4 3 19 19<= > br>46 13 19 19

However, I cannot find any parameters for the 46 13 1= > 9 19 group or the 4 3 19 19. Similarly, are there
any suggestions for w= > hat I can do here? Are there any issues with the atom types I have selected= > for
tetrolic acid? The two triple bonded C have given me some concern.= >



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> ------=_Part_6882799_1229177045.1418005247965-- > > From owner-chemistry@ccl.net Mon Dec 8 11:59:01 2014 From: "Bhaskar Kamble bkamble+*+rhrk.uni-kl.de" To: CCL Subject: CCL: Error message in EOMCCSD calculation in GAMESS Message-Id: <-50802-141208115035-32452-2wsPTNjnNjOuiRYHUeIXmg_._server.ccl.net> X-Original-From: "Bhaskar Kamble" Date: Mon, 8 Dec 2014 11:50:33 -0500 Sent to CCL by: "Bhaskar Kamble" [bkamble^^^rhrk.uni-kl.de] I am running an EOM-CCSD program in GAMESS and everything till the ROHF and CCSD is fine. However the program is aborted once the EOM-CCSD stage is reached and I get the following message: ********************************* THE EOMCC POINT GROUP IS CS GROUND STATE SYMETRY IS A' SIZE OF CIS PROBLEM: 1892 DDI Process 0: trapped a segmentation fault (SIGSEGV). ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). ********************************* Does anyone know what this means and how to fix the error? Any help would be greatly appreciated. Regards, Bhaskar Kamble From owner-chemistry@ccl.net Mon Dec 8 14:38:00 2014 From: "Sergio Manzetti sergio.manzetti=outlook.com" To: CCL Subject: CCL: Tutorial for CNTsimulation in GROMACS Message-Id: <-50803-141208143731-12397-hEB99NJTILi2NMW/jy0j9Q _ server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Mon, 8 Dec 2014 14:37:30 -0500 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] Dear all, does anyone know of a tutorial for making ITP and TOP files for GROMACS sims of carbon nanotubes? I have checked with the GRomacs mail ring, but to no avail (except for receiving an answer from a Hannibal Lecter) - so you can imagine what a hopeful stimulus that was. Appreciate any help! All the best From owner-chemistry@ccl.net Mon Dec 8 16:03:00 2014 From: "Arthur Zalevsky aozalevsky[*]gmail.com" To: CCL Subject: CCL: Tutorial for CNTsimulation in GROMACS Message-Id: <-50804-141208160140-19876-XoD/hx10ws1Pgm8iiiAYnw=server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: multipart/alternative; boundary=f46d044401b24b4bdc0509babbc2 Date: Tue, 9 Dec 2014 01:01:34 +0400 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky*_*gmail.com] --f46d044401b24b4bdc0509babbc2 Content-Type: text/plain; charset=UTF-8 Try: http://erg.biophys.msu.ru/wordpress/archives/186 Arthur 2014-12-08 22:37 GMT+03:00 Sergio Manzetti sergio.manzetti=outlook.com < owner-chemistry+/-ccl.net>: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] > Dear all, does anyone know of a tutorial for making ITP and TOP files for > GROMACS sims of carbon nanotubes? I have checked with the GRomacs mail > ring, but to no avail (except for receiving an answer from a Hannibal > Lecter) - so you can imagine what a hopeful stimulus that was. > > Appreciate any help! > > All the best> > > --f46d044401b24b4bdc0509babbc2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

2014-12-08 22:37 GMT+03:00 Sergio Manzetti sergio.manzetti=3Doutlook.com <owner-chemistry+/-ccl.net= >:

Sent to CCL by: "Sergio=C2=A0 Manzetti" [sergio.manzetti#outlook.com]
Dear all, does anyone know of a tutorial for making ITP and TOP files for G= ROMACS sims of carbon nanotubes? I have checked with the GRomacs mail ring,= but to no avail (except for receiving an answer from a Hannibal Lecter) - = so you can imagine what a hopeful stimulus that was.

Appreciate any help!

All the best



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--f46d044401b24b4bdc0509babbc2-- From owner-chemistry@ccl.net Mon Dec 8 16:50:01 2014 From: "conor douglas parks coparks2012(0)gmail.com" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50805-141208164839-26893-JrI6RUigVRAaLU7s7WzPxg/./server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 8 Dec 2014 16:48:38 -0500 Sent to CCL by: "conor douglas parks" [coparks2012*|*gmail.com] Hello, So I did some digging into the charmm parameters. Specifically, I was looking at the cgenFF. They do not seem to have the spC-spC-carbonyl C either. Do you think it would be okay to approximate the carbonyl C as the C from the CH3 group? Also in charmm, they don't seem to have the improper dihedral for the sp carbon, carbonyl C, carbonyl O, and hydroxyl oxygen group. However, if i just replace the sp carbon with a sp3 carbon the parameters exist. I was thinking if I was going to have to apply these approximations with the Charmm potential, it might make more sense to just make these approximations with the OPLS potential and not have to mix OPLS and charmm. Do you have any thoughts on this? conor > "Simon Halstead joyjoyhappyjoy-,-yahoo.co.uk" wrote: > > Sent to CCL by: Simon Halstead [joyjoyhappyjoy:-:yahoo.co.uk] > ------=_Part_6882799_1229177045.1418005247965 > Content-Type: text/plain; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > > Hi, > the choice of atoms looks reasonable - a quick way to check would be to mak= > e sure all the charges sum to zero.The problem you have is that OPLS doesn'= > t include every possible combination of functional groups - an alkyne to ca= > rboxylic acid is perhaps not very common. You have a few choices about what= > to do. > First, you could constrain part of the molecule which is a good choice if t= > he structure of that area is not likely to fluctuate much.Second, you could= > look for additional parameters in the literature. There are many papers pr= > oviding additional or improved OPLS parameters. For example, The Journal of= > Physical Chemistry B - Computational Study of Solvent Effects on the Molec= > ular Self-Assembly of Tetrolic Acid in Solution and Implications for the Po= > lymorph Formed from Crystallization (ACS Publications) provides some parame= > ters you could use (though this is a mixture of CHARMM and OPLS).Finally, y= > ou could calculate extra parameters yourself using some higher levels of th= > eory. > > Good luck, > Simon > From: conor douglas parks coparks2012=3Dgmail.com l.net> > To: "Halstead, Simon " =20 > Sent: Monday, December 8, 2014 7:10 AM > Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid > =20 > > Sent to CCL by: "conor douglas parks" [coparks2012.{=}.gmail.com] > Hello, I am in the process of performing my first molecular dynamics simula= > tions for an actual research=20 > project, and have some questions regarding the choice of the appropriate fo= > rce field parameters from=20 > the OPLS parameter set. My molecule is Tetrolic acid, and has what I believ= > e are the following atom=20 > types > > > atom#=C2=A0 =C2=A0 atom type=C2=A0 =C2=A0 =C2=A0 atom symbol=C2=A0 =C2=A0 = > =C2=A0 description > 209=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid COOH > 210=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 O=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid C=3DO > 211=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 OH=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid -OH > 212=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HO=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 carboxylic acid -COOH > 769=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 19=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CZ=C2=A0 =C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 alkyne RCCR > 80=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 13=C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CT=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Alkane CH3 > 85=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 46=C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HC=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 alkane H-C > > Now from what I can tell, I believe the following angles need to be specifi= > ed for Tetrolic acid > > 4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0=20 > 3=C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 7 > 4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 19 > 13=C2=A0 19=C2=A0 19 > 19=C2=A0 19=C2=A0 3 > 19=C2=A0 13=C2=A0 46 > > I can not find any parameters for the angle bending for the 19-19-3 angle i= > n the OPLS parameter set=20 > (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone h= > ave any suggestions of=20 > how I could obtain a suitable parameter for this type of interaction? > > Similary for the torsion, I believe I need parameters for > > 4 3 5 7 > 7 5 3 19 > 4 3 19 19 > 46 13 19 19 > > However, I cannot find any parameters for the 46 13 19 19 group or the 4 3 = > 19 19. Similarly, are there=20 > any suggestions for what I can do here? Are there any issues with the atom = > types I have selected for=20 > tetrolic acid? The two triple bonded C have given me some concern. > > > > -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 > =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------ =_Part_6882799_1229177045.1418005247965 > Content-Type: text/html; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > >
lveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;fo= > nt-size:14px">
Hi,
=3D"yui_3_16_0_1_1418003648379_3261">
003648379_3262" dir=3D"ltr">the choice of atoms looks reasonable - a quick = > way to check would be to make sure all the charges sum to zero.
d=3D"yui_3_16_0_1_1418003648379_3263" dir=3D"ltr">The problem you have is t= > hat OPLS doesn't include every possible combination of functional groups - = > an alkyne to carboxylic acid is perhaps not very common. You have a few cho= > ices about what to do.
=3D"ltr">
= > First, you could constrain part of the molecule which is a good choice if t= > he structure of that area is not likely to fluctuate much.
yui_3_16_0_1_1418003648379_3243" dir=3D"ltr">Second, you could look for add= > itional parameters in the literature. There are many papers providing addit= > ional or improved OPLS parameters. For example, 03648379_3242" href=3D"http://pubs.acs.org/doi/pdf/10.1021/jp7106582">The J= > ournal of Physical Chemistry B - Computational Study of Solvent Effects on = > the Molecular Self-Assembly of Tetrolic Acid in Solution and Implications f= > or the Polymorph Formed from Crystallization (ACS Publications) provide= > s some parameters you could use (though this is a mixture of CHARMM and OPL= > S).
Finally, y= > ou could calculate extra parameters yourself using some higher levels of th= > eory.

>
Good l= > uck,

<= > span>Simon

yle=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida= > Grande, sans-serif; font-size: 14px;">
79_3794" style=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Ar= > ial, Lucida Grande, sans-serif; font-size: 16px;">
1418003648379_3793" dir=3D"ltr">
1418003648379_5747" face=3D"Arial" size=3D"2"> t:bold;">From: conor douglas parks coparks2012=3Dgmail.com <o= > wner-chemistry{=}ccl.net>
To: pan> "Halstead, Simon " <joyjoyhappyjoy{=}yahoo.co.uk>
= > Sent: Monday, December 8,= > 2014 7:10 AM
Subject:= > CCL: Choosing appropriate OPLS parameters for Tetrolic Acid
 div>


Sent to CCL by: "conor douglas = > parks" [ s2012.{=}.gmail.com">coparks2012.{=}.gmail.com]
Hello, I am in the proce= > ss of performing my first molecular dynamics simulations for an actual rese= > arch
project, and have some questions regarding the choice of the appro= > priate force field parameters from
the OPLS parameter set. My molecule = > is Tetrolic acid, and has what I believe are the following atom
types r>

atom#    atom type      atom symbol&nb= > sp;     description
209          3&nb= > sp;                     &= > nbsp;   C                carb= > oxylic acid COOH
210          4    &n= > bsp;                     = > O                carboxylic acid C= > =3DO
211          5        = >                   OH  &nb= > sp;           carboxylic acid -OH
212  &n= > bsp;       7             = >             HO        &n= > bsp;     carboxylic acid -COOH
769       = >   19                  &n= > bsp;     CZ              alky= > ne RCCR
80            13    &nbs= > p;                   CT  = >             Alkane CH3
85    &n= > bsp;       46             = > ;           HC          &= > nbsp;   alkane H-C

Now from what I can tell, I believe the fol= > lowing angles need to be specified for Tetrolic acid

4    = > 3      5   
3    5    &nb= > sp; 7
4    3    19
13  19  19
19&n= > bsp; 19  3
19  13  46

I can not find any param= > eters for the angle bending for the 19-19-3 angle in the OPLS parameter set= >
( " target=3D"_blank">http://dasher.wustl.edu/ffe/distribution/params/oplsaa.= > prm). Does anyone have any suggestions of
how I could obtain a suit= > able parameter for this type of interaction?

Similary for the torsio= > n, I believe I need parameters for

4 3 5 7
7 5 3 19
4 3 19 19<= > br>46 13 19 19

However, I cannot find any parameters for the 46 13 1= > 9 19 group or the 4 3 19 19. Similarly, are there
any suggestions for w= > hat I can do here? Are there any issues with the atom types I have selected= > for
tetrolic acid? The two triple bonded C have given me some concern.= >



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> ------=_Part_6882799_1229177045.1418005247965-- > > From owner-chemistry@ccl.net Mon Dec 8 21:57:01 2014 From: "Rajib Biswas chemrajib++gmail.com" To: CCL Subject: CCL: Tutorial for CNTsimulation in GROMACS Message-Id: <-50806-141208174906-2410-UF67hm5HsP9S9C1EfoHgcg{:}server.ccl.net> X-Original-From: Rajib Biswas Content-Type: multipart/alternative; boundary=001a11c23d287804d40509bc3b8b Date: Mon, 8 Dec 2014 16:48:19 -0600 MIME-Version: 1.0 Sent to CCL by: Rajib Biswas [chemrajib ~~ gmail.com] --001a11c23d287804d40509bc3b8b Content-Type: text/plain; charset=UTF-8 You can try this http://chembytes.wikidot.com/grocnt On Mon, Dec 8, 2014 at 3:01 PM, Arthur Zalevsky aozalevsky[*]gmail.com < owner-chemistry ~ ccl.net> wrote: > Try: http://erg.biophys.msu.ru/wordpress/archives/186 > > Arthur > > 2014-12-08 22:37 GMT+03:00 Sergio Manzetti sergio.manzetti=outlook.com < > owner-chemistry(a)ccl.net>: > >> >> Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] >> Dear all, does anyone know of a tutorial for making ITP and TOP files for >> GROMACS sims of carbon nanotubes? I have checked with the GRomacs mail >> ring, but to no avail (except for receiving an answer from a Hannibal >> Lecter) - so you can imagine what a hopeful stimulus that was. >> >> Appreciate any help! >> >> All the best>> E-mail to subscribers: CHEMISTRY(a)ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST(a)ccl.net or use>> >> >> > --001a11c23d287804d40509bc3b8b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable


On Mon, Dec 8, 2014= at 3:01 PM, Arthur Zalevsky aozalevsky[*]gmai= l.com <owner-chemistry ~ ccl.net> wrote:

2014-12-08 22:37 GMT+03:00 = Sergio Manzetti sergio.manzetti=3Doutlook.com <owner-chemistry(a)ccl.net>:=

Sent to CCL by: "Sergio=C2=A0 Manzetti" [sergio.manzetti#outlook.com]
Dear all, does anyone know of a tutorial for making ITP and TOP files for G= ROMACS sims of carbon nanotubes? I have checked with the GRomacs mail ring,= but to no avail (except for receiving an answer from a Hannibal Lecter) - = so you can imagine what a hopeful stimulus that was.

Appreciate any help!

All the best



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--001a11c23d287804d40509bc3b8b--