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: jalem...@vt.edu
> To: gmx-users@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
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