[gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Jonathan Saboury]

Thanks as always Justin!

I'll be learning how to use CGenFF now then!

- Jonathan

On Sun, Mar 12, 2017 at 5:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/12/17 8:21 PM, Jonathan Saboury wrote:
>
>> Sorry for the delay, I didn't see this email.
>>
>> I don't believe it is a problem with gromacs, but a problem with
>> cgenff_charmm2gmx.py from (from
>> http://mackerell.umaryland.edu/download.php?filename=CHARMM_
>> ff_params_files/cgenff_charmm2gmx.py
>> )
>>
>> cgenff_charmm2gmx.py wrote the .pdb atom names from columns 14-17 instead
>> of 13-16. This code works fine if the atom names in .str outputted by
>> https://cgenff.paramchem.org/initguess/ is <=3 chars long. If it is 4
>> chars
>> long (one char in the atom name will be in column 17, which isn't read by
>> gromacs, and it shouldn't) the gromacs errs because the gmx outputed pdbs
>> (from editconf, solvate, the the like)  does not match the atom name in
>> .top.
>>
>> I have contacted them about this error.
>>
>>
> I fixed the script.  Please get the new version from our website.
>
> Note that the CGenFF server still produces old (version 3.0.1) topologies
> and is therefore not compatible with our C36/CGenFF 4.0 force field files.
> We're working on getting that updated but there are technical issues
> holding things back.
>
> -Justin
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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