[gmx-users] question on ffG43a1p force field

[Lei Qian]

Could I ask one more question about your *gromos43a1p.ff* force filed ?
Thanks!
I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce

It shows a fatal error:
"Fatal error:
The residues in the chain xxx--xxx do not have a consistent type. The first
residue has type 'Protein', while residue *SEP is of type 'Other'*.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the *residuetypes.dat file* in the
GROMACS library directory."

Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
"SEP   protein" to the list.
However, the fatal error still shows up after this change.
Could I ask how to solve this problem?
Thanks!





On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/16/19 2:15 AM, Lei Qian wrote:
> > Sorry for this basic question.
> > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
> > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also
> tried
> > to create a file called forcefield.doc and wrote "ffG43a1p" into it.
> > I put these files in working directory
> > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of
> > them worked.
> > Could I ask how to solve this problem?
>
> It sounds like you are trying to modify a very old and outdated version
> of the files (potentially with an outdated version of GROMACS - FF.dat
> is no longer used). The files you want for any post-4.0 version of
> GROMACS are in:
>
> http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
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