From owner-chemistry@ccl.net Sun Dec 7 18:22:01 2014 From: "conor douglas parks coparks2012=gmail.com" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50797-141207181013-20627-fzTxyaCvmhbO8RD7tOGhGA**server.ccl.net> X-Original-From: "conor douglas parks" Date: Sun, 7 Dec 2014 18:10:12 -0500 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 parameter set. My molecule is Tetrolic acid, and has what I believe are the following atom types atom# atom type atom symbol description 209 3 C carboxylic acid COOH 210 4 O carboxylic acid C=O 211 5 OH carboxylic acid -OH 212 7 HO carboxylic acid -COOH 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 specified for Tetrolic acid 4 3 5 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 in the OPLS parameter set (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone have any suggestions of 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 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 have given me some concern. From owner-chemistry@ccl.net Sun Dec 7 20:29:01 2014 From: "Elvis Martis elvis_bcp- -elvismartis.in" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50798-141207201638-31502-o2LRqvua0b2E4Hx9jgDl1A++server.ccl.net> X-Original-From: Elvis Martis Content-Type: multipart/alternative; boundary="_D70DBD85-A969-42B9-A9C8-FFDADF20AB06_" Date: Mon, 8 Dec 2014 06:46:08 +0530 MIME-Version: 1.0 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" 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"
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.
From: conor douglas parks copar= ks2012=3Dgmail.com
Sent: =E2=80=8E08-=E2=80=8E12-=E2= =80=8E2014 06:18
To: Martis, Elvis Martis
Subject: 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=3DO211          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 Sun Dec 7 21:23:00 2014 From: "Simon Halstead joyjoyhappyjoy-,-yahoo.co.uk" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50799-141207212055-21749-8jw26Kxcgumhn/98xH6KSQ,server.ccl.net> X-Original-From: Simon Halstead Content-Type: multipart/alternative; boundary="----=_Part_6882799_1229177045.1418005247965" Date: Mon, 8 Dec 2014 02:20:47 +0000 (UTC) MIME-Version: 1.0 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 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
Hi,

the choice of atoms looks reasonable - a quick = way to check would be to make sure all the charges sum to zero.
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.

= 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 add= itional parameters in the literature. There are many papers providing addit= ional or improved OPLS parameters. For example, 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

From: conor douglas parks coparks2012=3Dgmail.com <o= wner-chemistry{=}ccl.net>
To: "Halstead, Simon " <joyjoyhappyjoy{=}yahoo.co.uk>
= Sent: Monday, December 8,= 2014 7:10 AM
Subject:= CCL: Choosing appropriate OPLS parameters for Tetrolic Acid


Sent to CCL by: "conor douglas = parks" [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

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=
(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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