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

[Justin Lemkul]

On 11/26/18 12:54 PM, Francesco Pietra wrote:
> 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

You need a sensible name in your @TRIPOS<MOLECULE> definition, with no 
more than 4 characters. Your file has the name of a full path to a file 
in it.

-Justin

> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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