From owner-chemistry@ccl.net Fri Aug 14 00:23:00 2009 From: "Natalia Zakharova nlzakh,,wsu.edu" To: CCL Subject: CCL: CHARMM: total charge not an integer Message-Id: <-39994-090813174315-23199-DhwmOOWA/ZR45mIP1buIUQ[#]server.ccl.net> X-Original-From: "Natalia Zakharova" Date: Thu, 13 Aug 2009 17:43:11 -0400 Sent to CCL by: "Natalia Zakharova" [nlzakh^_^wsu.edu] I am currently trying to perform CHARMM (version c32b2) calculation for a tri-peptide WGY (Trp-Gly-Tyr) with tryptophan side chain protonated at nitrogen. When attmepting to run CHARMM, I get the following error: ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 1 TITRATABLE GROUPS THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF HIS - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 1 CHARMM> GENErate wgyneutral FIRST NNUT LAST CNUT SETup THE PATCH 'NNUT' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CNUT' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is WGYNEUTR. Warning from PSFSUM: The sum of charges ( 1.090000) is not an integer ***** LEVEL 0 WARNING FROM ***** ***** Total charge not an integer I absolutely have no idea how to fix this issue and any help will be appreciated. Thank you, Natalia Zakharova From owner-chemistry@ccl.net Fri Aug 14 00:58:01 2009 From: "Bhalchandra Pujari bspujari-$-gmail.com" To: CCL Subject: CCL: Software for calculation DOS and PDOS Message-Id: <-39995-090813232204-4441-EsrbTOuQoObhzitdoXSUTg : server.ccl.net> X-Original-From: Bhalchandra Pujari Content-Type: multipart/alternative; boundary=0003255750f680340a0471118db3 Date: Fri, 14 Aug 2009 08:51:29 +0530 MIME-Version: 1.0 Sent to CCL by: Bhalchandra Pujari [bspujari+/-gmail.com] --0003255750f680340a0471118db3 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, Most of the softwares like Quantum Espresso or VASP have such facilities. regards On Fri, Aug 14, 2009 at 1:43 AM, Morad M El-Hendawy M80elhendawy],[yahoo.co= m wrote: > > Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy::yahoo.com] > Hi every body, > I wonder if anyone tell me about a reputed software for calculating Densi= ty > Of State (DOS) and Partial Density Of State (PDOS) > My regards > Morad El-Hendawy > Ireland > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 --~~----~----~-------~---~~---~----~~---~----~--~--- Bhalchandra S Pujari. (=E0=A4=AD=E0=A4=BE=E0=A4=B2=E0=A4=9A=E0=A4=82=E0=A4=A6=E0=A5=8D=E0=A4=B0 = =E0=A4=AA=E0=A5=81=E0=A4=9C=E0=A4=BE=E0=A4=B0=E0=A5=80) Senior Research Fellow (CSIR), Advanced Computing Laboratory, Department of Physics, Pune University, Pune 411007. INDIA (+91 20) 25692678; Extn# 408 http://bspujari.googlepages.com http://photokatta.blogspot.com/ --~~----~----~-------~---~~---~----~~---~----~--~--- --0003255750f680340a0471118db3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi,
=C2=A0Most of the softwares like Quantum Espresso or VASP have such = facilities.

regards


On Fri, Au= g 14, 2009 at 1:43 AM, Morad M El-Hendawy M80elhendawy],[yahoo.com <owner-chemistry[-]ccl.net> wrote:

Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy::yahoo.com]
Hi every body,
I wonder if anyone tell me about a reputed software for calculating Density= Of State (DOS) and Partial Density Of State (PDOS)
My regards
Morad El-Hendawy
Ireland



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--
--~~----~----~-------~-= --~~---~----~~---~----~--~---
Bhalchandra S Pujari.
(=E0=A4=AD=E0=A4= =BE=E0=A4=B2=E0=A4=9A=E0=A4=82=E0=A4=A6=E0=A5=8D=E0=A4=B0 =E0=A4=AA=E0=A5= =81=E0=A4=9C=E0=A4=BE=E0=A4=B0=E0=A5=80)

Senior Research Fellow (CSI= R),
Advanced Computing Laboratory,
Department of Physics,
Pune University, Pune 411007.
INDIA

(+9= 1 20) 25692678; Extn# 408

http://bspujari.googlepages.com
http://photokatta.blogspot.com/
--~~----~----~-------~---~~---~----~~---~----~--~---
--0003255750f680340a0471118db3-- From owner-chemistry@ccl.net Fri Aug 14 03:37:01 2009 From: "Nilesh Tawari tawari.nilesh,,gmail.com" To: CCL Subject: CCL: heavy atoms Message-Id: <-39996-090814032738-27978-5D/tWg1vrepnJbkv8NqSgw*server.ccl.net> X-Original-From: Nilesh Tawari Content-Type: multipart/alternative; boundary=00504502b870e54a14047114e973 Date: Fri, 14 Aug 2009 12:52:24 +0530 MIME-Version: 1.0 Sent to CCL by: Nilesh Tawari [tawari.nilesh#,#gmail.com] --00504502b870e54a14047114e973 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit hi, You can use any database manegment tool like ISIS, Chem office finder or Instant Jchem (free for academic) to store ur database and then do substructure query in that. -nilesh On Thu, Aug 13, 2009 at 11:30 PM, amit dong dongamit123~!~gmail.com < owner-chemistry%%ccl.net> wrote: > Hi, > > I need to search for analogs of a compound in a database. Is there any tool > that I can use for this purpose. > > Thanks > AD > > > -- Mr. Nilesh R. Tawari PhD (Tech) Medicinal Chemistry ICT, Matunga (E), Mumbai-19 --00504502b870e54a14047114e973 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
hi,
You can use any database manegment tool like ISIS, Chem office finder or Instant Jchem (free for academic) to store ur database and then do substructure query in that.
-nilesh

On Thu, Aug 13, 2009 at 11:30 PM, amit dong dongamit123~!~gmail.com <owner-chemistry%%ccl.net> wrote:
Hi,

I need to search for analogs of a compound in a database. Is there any tool that I can use for this purpose.

Thanks
AD





--
Mr. Nilesh R. Tawari
PhD (Tech) Medicinal Chemistry
ICT, Matunga (E), Mumbai-19
--00504502b870e54a14047114e973-- From owner-chemistry@ccl.net Fri Aug 14 04:11:01 2009 From: "Daniil Bratashov dn2010||gmail.com" To: CCL Subject: CCL: ZINDO compilation saga continues Message-Id: <-39997-090814033342-28575-fSfG2QvFy/lvDJnqLzkWdA(-)server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 14 Aug 2009 09:27:09 +0400 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010||gmail.com] On Thu, 13 Aug 2009 09:03:20 -0400 "John McKelvey jmmckel(!)gmail.com" wrote: > I downloaded the Windows version, but GCC complains > about no stdio.h !!!! Most Bazaar!!! Anyone tried Gfort/GCC on > Windows and gotten GCC to work? You need either MinGW/MSYS set of tools for unix application porting on windows, or Cygwin --- complete unix system emulation. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Fri Aug 14 06:29:01 2009 From: "Cory Pye cpye=crux.smu.ca" To: CCL Subject: CCL: Split peak in spectra of water Message-Id: <-39998-090814060643-30312-BkHH/lMjD7Z4aERGWsahEg-.-server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 14 Aug 2009 07:06:22 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye ~ crux.smu.ca] Hi, I have a couple of ideas. Clearly the vibrational spectra of the water molecules that are strongly bound to the metal will have different frequencies. In a few cases, they can even be experimentally deconvoluted or even appear as separate peaks (Al, Be come to mind). In most cases, however, they are not far enough away from the pure water peaks to be discerned from the broad water absorption. For your particular ion, Sn(II), which has an inert s2 pair, not all of the water in the inner hydration shell will necessarily be equivalent. Suppose Sn(II) was octahedral, then I would expect a distortion from the ideal Th symmetry to something like C3v or C3 (See analogous bismuth system: Pye et al, Can J Chem, 85, p945-950 (2007) ). In that case, you form two sets of three equivalent water molecules which might have different vibrational properties. These two sets of waters might interconvert en masse by a sort of partial umbrella motion. If the timescale for this motion is larger than the time for a vibration, then you would expect to see two sets of peaks for the inner shell waters. It is difficult to pin this down further without further information. I don't know if you can animate the vibrational mode itself from an MD simulation, say by taking a narrow frequency slice and inverse Fourier-transforming it, as I don't have any MD experience whatsoever. I hope this helps in some small way. On Thu, 13 Aug 2009, Len Villamin Lim murdockdx(~)yahoo.com wrote: > > Sent to CCL by: "Len Villamin Lim" [murdockdx_+_yahoo.com] > I'm working on computer simulations of metal ions in solution using a hybrid QM/MM framework. One thing that interested me is the IR spectra of water molecules near the ion and I've tried to generate spectra via FT of autocorrelation functions of the normal modes. I'm relatively new to the idea, but I was able to get (more or less) sensible values for the frequencies (e.g. ~3900/cm for H2O symmetric stretch). It puzzles me though that for one particular ion (Sn(II)) I get small side peaks for the stretching frequencies for 1st and 2nd shell water molecules. Can someone help me figure it out? (is there some known mistakes that lead to this? or is there likely to be some vibrational coupling involved?). I'd appreciate the help. > > > Len Herald Lim > len.lim###student.uibk.ac.at > University of Innsbruck > Innrain 52a > A-6020 Innsbruck> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye,,crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Fri Aug 14 09:32:01 2009 From: "Len Lim murdockdx*|*yahoo.com" To: CCL Subject: CCL: Split peak in spectra of water Message-Id: <-39999-090814085912-23670-S1LT/g4zkYe2XbW9OVgVBw[]server.ccl.net> X-Original-From: Len Lim Content-Type: multipart/alternative; boundary="0-2025935615-1250251139=:33365" Date: Fri, 14 Aug 2009 04:58:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Len Lim [murdockdx###yahoo.com] --0-2025935615-1250251139=:33365 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello, Yes, you have helped me a lot. That is indeed the case for Sn(II) (two diff= erent sets of ~4 equivalent waters) and we have been able to track the moti= on of the first hydration layer (although quite primitively) from the MD tr= ajectories, but I guess we really haven't figured out how to estimate its t= imescale. However, after looking into Pb(II), I also found some split peaks= in the second shell. Pb(II) is a bit too large to really show the influenc= e of the inert s2 pair, especially it the second shell region. But thank yo= u very much for the helpful insight . Len Herald Lim len.lim{:}student.uibk.ac.at =0A =0A University of Innsbruck =0A Innrain 52a =0A A-6020=0A =0A Innsbruck =0A =0A =0A phone: +43(0)512/507-5161 =0A fax: +43(0)512/507-2714 --- On Fri, 8/14/09, Cory Pye cpye=3Dcrux.smu.ca = wrote: > From: Cory Pye cpye=3Dcrux.smu.ca Subject: CCL: Split peak in spectra of water To: "Lim, Len Villamin " Date: Friday, August 14, 2009, 3:06 AM Sent to CCL by: Cory Pye [cpye ~ crux.smu.ca] Hi, I have a couple of ideas. Clearly the vibrational spectra of the water molecules that are strongly bound to the metal will have different frequenc= ies. In a few cases, they can even be experimentally deconvoluted or even appear= as separate peaks (Al, Be come to mind). In most cases, however, they are not = far enough away from the pure water peaks to be discerned from the broad water absorption. For your particular ion, Sn(II), which has an inert s2 pair, not all of the water in the inner hydration shell will necessarily be equivalent. Suppose Sn(II) was octahedral, then I would expect a distortion from the ideal Th symmetry to something like C3v or C3 (See analogous bismuth system: Pye et = al, Can J Chem, 85, p945-950 (2007) ). In that case, you form two sets of three equivalent water molecules which might have different vibrational propertie= s. These two sets of waters might interconvert en masse by a sort of partial umbrella motion. If the timescale for this motion is larger than the time f= or a vibration, then you would expect to see two sets of peaks for the inner s= hell waters. It is difficult to pin this down further without further information. I don= 't know if you can animate the vibrational mode itself from an MD simulation, = say by taking a narrow frequency slice and inverse Fourier-transforming it, as = I don't have any MD experience whatsoever. I hope this helps in some small way. On Thu, 13 Aug 2009, Len Villamin Lim murdockdx(~)yahoo.com wrote: > > Sent to CCL by: "Len Villamin Lim" [murdockdx_+_yahoo.com] > I'm working on computer simulations of metal ions in solution using a hyb= rid QM/MM framework. One thing that interested me is the IR spectra of wate= r molecules near the ion and I've tried to generate spectra via FT of autoc= orrelation functions of the normal modes. I'm relatively new to the idea, b= ut I was able to get (more or less) sensible values for the frequencies (e.= g. ~3900/cm for H2O symmetric stretch). It puzzles me though that for one p= articular ion (Sn(II)) I get small side peaks for the stretching frequencie= s for 1st and 2nd shell water molecules. Can someone help me figure it out?= (is there some known mistakes that lead to this? or is there likely to be = some vibrational coupling involved?). I'd appreciate the help. > > > Len Herald Lim > len.lim###student.uibk.ac.at > University of Innsbruck > Innrain 52a > A-6020 Innsbruck> > =A0=A0=A0*************=A0 =A0 !=A0 Dr. Cory C. Pye *****************=A0 !=A0 Associate Professor ***=A0=A0=A0**=A0 =A0 **=A0 **=A0 !=A0 Theoretical and Computational Chemis= try **=A0=A0=A0*=A0 ****=A0 =A0 =A0 =A0 !=A0 Department of Chemistry, Saint Mar= y's University **=A0 =A0 =A0 *=A0 *=A0 =A0 =A0 =A0 !=A0 923 Robie Street, Halifax, NS B3H = 3C3 **=A0 =A0 =A0 *=A0 *=A0 =A0 =A0 =A0 !=A0 cpye-x-crux.stmarys.ca=A0=A0=A0htt= p://apwww.stmarys.ca/~cpye ***=A0 =A0=A0=A0*=A0 *=A0 =A0 **=A0 !=A0 Ph: (902)-420-5654=A0 FAX:(902)-49= 6-8104 *****************=A0 ! =A0=A0=A0*************=A0 =A0 !=A0 Les Hartree-Focks (Apologies to Montreal= Canadien Fans) -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-2025935615-1250251139=:33365 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,
Yes, you have helped me a lot. That= is indeed the case for Sn(II) (two different sets of ~4 equivalent waters)= and we have been able to track the motion of the first hydration layer (al= though quite primitively) from the MD trajectories, but I guess we really h= aven't figured out how to estimate its timescale. However, after looking in= to Pb(II), I also found some split peaks in the second shell. Pb(II) is a b= it too large to really show the influence of the inert s2 pair, especially = it the second shell region. But thank you very much for the helpful insight= .

Len Herald Lim
l= en.lim{:}student.uibk.ac.at

=0A = =0A = University of Innsbruck
=0A Innrain 52a
=0A = A-6020=0A =0A Innsbruck
=0A

=0A

=0A= phone: +43(0)512/507-5161
=0A fax: +43(0)512/= 507-2714



--- On Fri, 8/14/09, Cory Pye cpye=3Dcrux.smu.ca = <owner-chemistry{:}ccl.net> wrote:
=
From: Cory Pye cpye=3Dcrux.smu.ca <owner-chemistry{:}ccl.net>
Su= bject: CCL: Split peak in spectra of water
To: "Lim, Len Villamin -id#3w= y-" <murdockdx{:}yahoo.com>
Date: Friday, August 14, 2009, 3:06 AM

Sent to CCL by: Cory Pye [cpye ~ crux.sm= u.ca]
Hi,
I have a couple of ideas. Clearly the vibrational spectra o= f the water
molecules that are strongly bound to the metal will have dif= ferent frequencies.
In a few cases, they can even be experimentally deco= nvoluted or even appear as
separate peaks (Al, Be come to mind). In most= cases, however, they are not far
enough away from the pure water peaks = to be discerned from the broad water
absorption.

For your particular ion, Sn(II), which has an = inert s2 pair, not all of the
water in the inner hydration shell will ne= cessarily be equivalent. Suppose
Sn(II) was octahedral, then I would exp= ect a distortion from the ideal Th
symmetry to something like C3v or C3 = (See analogous bismuth system: Pye et al,
Can J Chem, 85, p945-950 (2007= ) ). In that case, you form two sets of three
equivalent water molecules= which might have different vibrational properties.
These two sets of wa= ters might interconvert en masse by a sort of partial
umbrella motion. I= f the timescale for this motion is larger than the time for
a vibration,= then you would expect to see two sets of peaks for the inner shell
wate= rs.

It is difficult to pin this down further without further informa= tion. I don't
know if you can animate the vibrational mode itself from a= n MD simulation, say
by taking a narrow frequency slice and inverse Fourier-transforming it, as I
don't have any MD experience what= soever.

I hope this helps in some small way.
On Thu, 13 Aug 2009,= Len Villamin Lim murdockdx(~)yahoo.com wrote:

>
> Sent to = CCL by: "Len Villamin Lim" [murdockdx_+_yahoo.com]
> I'm working on c= omputer simulations of metal ions in solution using a hybrid QM/MM framewor= k. One thing that interested me is the IR spectra of water molecules near t= he ion and I've tried to generate spectra via FT of autocorrelation functio= ns of the normal modes. I'm relatively new to the idea, but I was able to g= et (more or less) sensible values for the frequencies (e.g. ~3900/cm for H2= O symmetric stretch). It puzzles me though that for one particular ion (Sn(= II)) I get small side peaks for the stretching frequencies for 1st and 2nd = shell water molecules. Can someone help me figure it out? (is there some kn= own mistakes that lead to this? or is there likely to be some vibrational coupling involved?). I'd appreciate the help.
>
><= br>> Len Herald Lim
> len.lim###student.uibk.ac.at
> Univers= ity of Innsbruck
> Innrain 52a
> A-6020 Innsbruck>
>
   *************    !  Dr. Cory C. Pye<= br> *****************  !  Associate Professor
***  &= nbsp;**    **  **  !  Theoretical and Computationa= l Chemistry
**   *  ****        = !  Department of Chemistry, Saint Mary's University
**   =   *  *        !  923 Robie Street, Hali= fax, NS B3H 3C3
**      *  *      &nb= sp; !  cpye-x-crux.stmarys.ca   http://apwww.stmarys.ca/~cpye***     *  *    **  !  Ph: (902)-420-5654  FAX:(902)-496-8104
*****************  !
&= nbsp;  *************    !  Les Hartree-Focks (Apol= ogies to Montreal Canadien Fans)



-=3D This is automatically = added to each message by the mailing script =3D-
To recover the email ad= dress of the author of the message, please change
the strange characters= on the top line to the {:} sign. You can also
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=0A=0A=0A=0A --0-2025935615-1250251139=:33365-- From owner-chemistry@ccl.net Fri Aug 14 12:13:01 2009 From: "Venable, Richard (NIH/NHLBI) E venabler * nhlbi.nih.gov" To: CCL Subject: CCL: CHARMM: total charge not an integer Message-Id: <-40000-090814121059-19433-ofpkhNDYzxiXdESuqv+NBA(!)server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 14 Aug 2009 12:10:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler\a/nhlbi.nih.gov] The forums at www.charmm.org can be quite helpful, esp. via the Search feat= ure. Molecules should have an integer charge; yours does not. Since chain termi= nal patches NNUT and CNUT are not part of the standard distribution, you sh= ould either look more closely at these two patch residues, or use more stan= dard pairs of end patches such as NTER/CTER (zwitterion) or ACE/CT3 (neutra= l, methyl). -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 8/13/09 5:43 PM, "Natalia Zakharova nlzakh,,wsu.edu" wrote: Sent to CCL by: "Natalia Zakharova" [nlzakh^_^wsu.edu] I am currently trying to perform CHARMM (version c32b2) calculation for a t= ri-peptide WGY (Trp-Gly-Tyr) with tryptophan side chain protonated at nitro= gen. When attmepting to run CHARMM, I get the following error: ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 1 TITRATABLE GROUPS THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND = RTF HIS - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 1 CHARMM> GENErate wgyneutral FIRST NNUT LAST CNUT SETup THE PATCH 'NNUT' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CNUT' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is WGYNEUTR. Warning from PSFSUM: The sum of charges ( 1.090000) is not an integer ***** LEVEL 0 WARNING FROM ***** ***** Total charge not an integer I absolutely have no idea how to fix this issue and any help will be apprec= iated. Thank you, Natalia Zakharova From owner-chemistry@ccl.net Fri Aug 14 16:21:00 2009 From: "Lev Gorenstein lev,,ledorub.poxod.com" To: CCL Subject: CCL: CHARMM: total charge not an integer Message-Id: <-40001-090814125551-24148-ZrLmDcMZjY0vZYu6Ha7ppw^_^server.ccl.net> X-Original-From: Lev Gorenstein Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 14 Aug 2009 12:01:10 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Lev Gorenstein [lev _ ledorub.poxod.com] On Thu, 13 Aug 2009, Natalia Zakharova wrote: NZn> I am currently trying to perform CHARMM (version c32b2) NZn> calculation for a tri-peptide WGY (Trp-Gly-Tyr) with tryptophan NZn> side chain protonated at nitrogen. When attmepting to run NZn> CHARMM, I get the following error: NZh NZn> ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 1 TITRATABLE GROUPS NZn> THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF NZn> HIS - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 1 NZn> NZn> CHARMM> GENErate wgyneutral FIRST NNUT LAST CNUT SETup NZn> THE PATCH 'NNUT' WILL BE USED FOR THE FIRST RESIDUE NZn> THE PATCH 'CNUT' WILL BE USED FOR THE LAST RESIDUE NZn> GENPSF> Segment 1 has been generated. Its identifier is WGYNEUTR. NZn> NZn> Warning from PSFSUM: The sum of charges ( 1.090000) is not an integer NZn> NZn> NZn> ***** LEVEL 0 WARNING FROM ***** NZn> ***** Total charge not an integer To ignore the level XXX flag in CHARMM, set the crytical error threshold BOMLEV to anything lower than XXX. So in your case, you could ignore the error by setting BOMLEV -1 (or even -2 if you are brave). Of course this is a very crude solution, and by sweeping the problem under the rug now you will not get reliable results later, so I wouldn't recommend it. It looks like there's something wrong in the setup, so you'd better investigate it. My suspicion is that the culprits are NNUT and CNUT patches in your 'generate' statement. I don't see them in the standard CHARMM topology and parameter files in our distribution of CHARMM. Are these some special patches developed in your lab? Standard zwitter-ion terminal patches in CHARMM are called NTER and CTER. To test whether the problem is with NNUT/CNUT, try replacing them (first both of them, then one by one) with standard CTER and NTER and see if that fixes the problem. And couple general notes as food for thoughts: 1) Are there any other warnings before this (maybe where you set up sequence and/or coordinates)? If so, you'll need to look at them, too. 2) CHARMM c32b2 is a pretty old version, so you might want to upgrade to a newer one (unless this is a continuation of the existing project where it's safer to do all calculations with exactly the same version of CHARMM and even the same binary ;-). Regards, Lev -- Prof. Carol Post lab Purdue University From owner-chemistry@ccl.net Fri Aug 14 17:57:00 2009 From: "Kaci Tizi_Ouzou kaci.tiziouzou]![gmail.com" To: CCL Subject: CCL: Metropolis/Monte-Carlo tutorial Message-Id: <-40002-090814013439-5392-l0mAsGbz4j5ZiLsEb4jP5A||server.ccl.net> X-Original-From: Kaci Tizi_Ouzou Content-Type: multipart/alternative; boundary=0015174bdc705ce5a6047112fd30 Date: Thu, 13 Aug 2009 23:04:40 -0600 MIME-Version: 1.0 Sent to CCL by: Kaci Tizi_Ouzou [kaci.tiziouzou-$-gmail.com] --0015174bdc705ce5a6047112fd30 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, Is there any good sites where I could find tutorials, algorithms for Metropolis/Monte Carlo techniques in chemistry. Thanks all, Cheers Kass --0015174bdc705ce5a6047112fd30 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all,

Is there any good sites where I could find tutorials, algorithms for Metropolis/Monte Carlo techniques in chemistry.

Thanks all,

Cheers

Kass
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