[gmx-users] Re: Problem with using topolbuild1_3.tgz

Wed Jan 26 23:29:13 CET 2011

On Sat, Jan. 22, 2011 at 1:44 AM, Sweta Iyer <iyer at wehi.EDU.AU> wrote:

> > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <iyer at wehi.EDU.AU> 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 <iyer at wehi.EDU.AU>
To: gmx-users at gromacs.org
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" <brucedray at yahoo.com>
> Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz
> To: gmx-users at gromacs.org
> Message-ID: <417950.70449.qm at web35801.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <iyer at wehi.EDU.AU> 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
>
>
>
>
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