On Sat, Jan. 22, 2011 at 1:44 AM, Sweta Iyer <[email protected]> wrote:
> > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <[email protected]> wrote: > >> Hi, I am trying to generate topology files for a set of lipids with the > >> help of topolbuild1_3.tgz package found at the other software page of > >> GROMACS website. > >> > >> I downloaded and installed all files and tried running the program with > >> a > >> MOL2 file with charges in it. However, it shows an error message as > >> follows: > >> > >> Fatal error. > >> Source code file: readmol2.c, line: 758 > >> Atom 1 (C) has 3 connections when allowed 0 > >> > >> I am not sure how to get over this problem! Wonder what will fix this > >> error and get the program running! > > > > A major requirement of topolbuild is that the mol2 file use correct atom > > types as defined by Tripos, whose file format mol2 is, and as used in > > Sybyl. > > The error message suggests that you have not specified correct Tripos > > Sybyl > > atom types. There may be other problems in your mol2 file as well. > > Correct the atom types and check that the file is otherwise syntactically > > correct and it should work. > > > > However, I believe that lipid topology files for gromacs are already >available > > for download. > > > > I hope that helps. > > Hi Bruce, > Thanx for the reply. The MOL2 file was generated by the RESP ESP charge > derive server. I did not check the file in SYBYL. However, structurally it > seems correct. I will try reading it into sybyl and then resave it into > another mol2 file. I am not familiar with that server. However, a Sybyl atom type for most atoms consists of the atomic symbol followed by a period followed by a number or a short character string. For example, C.3 is an sp3 hybridized carbon, N.ar is an aromatic ring nitrogen, and O.co2 is a carboxylic acid oxygen. I believe the file you have lacks the type designator after the atomic symbol for atom 1. > I am looking at making topology files for lipids like cardiolipin, di > myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and > myristoleic acid. DO you know of any available gromacs topology files for > these? I cannot help you on that, but would suggest you ask those who have published lipid simulations. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ________________________________ From: Sweta Iyer <[email protected]> To: [email protected] Sent: Sat, January 22, 2011 1:44:25 AM Subject: [gmx-users] Re: Problem with using topolbuild1_3.tgz > Date: Fri, 21 Jan 2011 06:55:30 -0800 (PST) > From: "Bruce D. Ray" <[email protected]> > Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <[email protected]> wrote: >> Hi, I am trying to generate topology files for a set of lipids with the >> help of topolbuild1_3.tgz package found at the other software page of >> GROMACS website. >> >> I downloaded and installed all files and tried running the program with >> a >> MOL2 file with charges in it. However, it shows an error message as >> follows: >> >> Fatal error. >> Source code file: readmol2.c, line: 758 >> Atom 1 (C) has 3 connections when allowed 0 >> >> I am not sure how to get over this problem! Wonder what will fix this >> error and get the program running! > > A major requirement of topolbuild is that the mol2 file use correct atom > types as defined by Tripos, whose file format mol2 is, and as used in > Sybyl. > The error message suggests that you have not specified correct Tripos > Sybyl > atom types. There may be other problems in your mol2 file as well. > Correct the atom types and check that the file is otherwise syntactically > correct and it should work. > > However, I believe that lipid topology files for gromacs are already > available > for download. > > I hope that helps. > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 Hi Bruce, Thanx for the reply. The MOL2 file was generated by the RESP ESP charge derive server. I did not check the file in SYBYL. However, structurally it seems correct. I will try reading it into sybyl and then resave it into another mol2 file. I am looking at making topology files for lipids like cardiolipin, di myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and myristoleic acid. DO you know of any available gromacs topology files for these? Cheers Sweta > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: >http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/bdd5ae9c/attachment.html >l > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 156 > ****************************************** > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. 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