[gmx-users] error with changing pdb file

[Justin A. Lemkul]

ksm tprk wrote:
> Hello Justin,
> 
> 
> I looked at in my gromacs/3.3.1 and it ahs only ffgmx.n2t force field 
> file. because of that, I chaged to new version gromacs.
> I tried to use different force filed but new version gromacs but they 
> didn't work.
> I used gromacs/4.0.5 and I created .gro and by using x2top but it give 
> below errors. If I use pdb2gmx, it gives me residue UNK error.
> First I used "GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)" but 
> it gave me below error:
> 
> 
> Can not find forcefield for atom C-1597 with 3 bonds
> Can not find forcefield for atom C-1598 with 3 bonds
> Can not find forcefield for atom C-1599 with 2 bonds
> Can not find forcefield for atom C-1600 with 2 bonds
> 
> -------------------------------------------------------
> Program x2top_mpi, VERSION 4.0.5
> Source code file: x2top.c, line: 207
> 
> Fatal error:
> Could only find a forcefield type for 0 out of 1600 atoms
> -------------------------------------------------------
> 
> 
> After that I used "OPLS-AA/L all-atom force field (2001 aminoacid 
> dihedrals)" and it gave me:
> 
> 
> Looking whether force field files exist
> Opening library file /opt/apps/gromacs/4.0.5/share/gromacs/top/ffoplsaa.rtp
> Opening library file ffoplsaa.n2t
> Opening library file ffoplsaa.n2t
> There are 25 name to type translations
> Generating bonds from distances...
> atom 1600
> Can not find forcefield for atom N-25 with 3 bonds
> 
> -------------------------------------------------------
> Program x2top_mpi, VERSION 4.0.5
> Source code file: x2top.c, line: 207
> 
> Fatal error:
> Could only find a forcefield type for 1599 out of 1600 atoms
> -------------------------------------------------------
> 
> 
> 
> And I tried "[DEPRECATED] Gromacs force field (see manual)" and "Encad 
> all-atom force field, using scaled-down vacuum charges". they gave me 
> same error at first.
> 

The 4.0.5 version of x2top is broken unless you use the -nopbc option, which, 
for the purposes of carbon nanotubes, is useless unless you specify all the 
cross-boundary bonded terms yourself.

You had a functional topology before, why are you starting over?  You didn't 
give a very clear description of the changes you were making that were inducing 
the grompp errors, and you stand a better chance of identifying those problems 
and solving them if you provide the information I asked for last time (relevant 
topology lines and the corresponding coordinate entries).

-Justin

> Thank you,
> Kasim
> 
> 
> 
> 
> 
> 
> 
> 
>  > Date: Thu, 17 Dec 2009 15:31:23 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] error with changing pdb file
>  >
>  >
>  >
>  > ksm tprk wrote:
>  > > I changed pdb file after that I generated topology file.
>  > >
>  >
>  > It appears you are relying on grompp to figure out what parameters 
> should be
>  > used for these angles, and apparently, given these atom types, there 
> are no
>  > default values available in the force field you've chosen to use. So 
> either
>  > specify parameters manually or use a different force field.
>  >
>  > If you need further advice, it would be useful to know the force 
> field you're
>  > trying to use and see the problematic lines of the topology alongside 
> the
>  > modified coordinate file.
>  >
>  > -Justin
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================