[gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

[Francesco Pietra]

Hurrying - as with my post above - is seldom a good procedure.
The next step, converting ligand_ini.pdb to ligand.gro did not work well,
i.e., for GDP the .gro file reads
S  C  A  M  O  R  G
   40
    0/scr    PB    1   0.100   0.000   0.100
    0/scr   O1B    2   0.100   0.000   0.100
    0/scr   O2B    3   0.100   0.000   0.100
    0/scr   O3B    4   0.100   0.000   0.100
    0/scr   O3A    5   0.100   0.000   0.100
    0/scr    PA    6   0.100   0.000   0.100

which came anyway unespected as the ligand_ini.pdb looks like to be correct

ATOM      1 PB   /scratch/phpK1JFey_GDP_H.pdb    1     320.960 448.853
308.012  1.00  0.00
ATOM      2 O1B  /scratch/phpK1JFey_GDP_H.pdb    1     320.256 449.824
307.091  1.00  0.00
ATOM      3 O2B  /scratch/phpK1JFey_GDP_H.pdb    1     320.922 447.397
307.609  1.00  0.00
ATOM      4 O3B  /scratch/phpK1JFey_GDP_H.pdb    1     320.622 449.126
309.460  1.00  0.00
ATOM      5 O3A  /scratch/phpK1JFey_GDP_H.pdb    1     322.508 449.269
307.860  1.00  0.00
ATOM      6 PA   /scratch/phpK1JFey_GDP_H.pdb    1     323.692 448.599
308.726  1.00  0.00
ATOM      7 O1A  /scratch/phpK1JFey_GDP_H.pdb    1     324.384 447.624
307.801  1.00  0.00 came unexpected, as the ligand_ini.pdb looks like to be
correct

fp

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Mon, Nov 26, 2018 at 6:25 PM
Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
versions
To: <gmx-users at gromacs.org>


This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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