[gmx-users] forcefield installation on GROMACS 5.1.4

[Justin Lemkul]

On 3/28/17 3:12 AM, Simon Kit Sang Chu wrote:
> Dear Justin,
>
> Thank you very much. I followed the same spirit and add forcefield.doc.
> However, it did not work until changing all ffPACE_1.5.rtp .ddb .....etc
> files into aminoacids.rpt .ddb ..... GROMACS seems to recognize only the
> name "aminoacids". Also, don't forget to change the ffPACE1.5.itp to
> *forcefield.itp* instead of aminoacids.itp.
>

That's not strictly true; the .rtp files can be named anything.  I don't know 
why you encountered problems, but many force fields use different names.  The 
naming scheme may require a match in base name between an .rtp and an .hdb file, 
but there is flexibility (for instance, we use "merged.rtp" in our CHARMM36 port 
because it's a lot of stuff in one file, not just protein residues).

-Justin

> Regards,
> Simon
>
> 2017-03-28 0:54 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 3/27/17 7:44 AM, Simon Kit Sang Chu wrote:
>>
>>> Hi everyone,
>>>
>>> Recently I am looking into PACE
>>> <https://www.ks.uiuc.edu/Research/cgfolding/> for my system and
>>> installation of forcefield is required. The files located inside the
>>> forcefield directory is given by -
>>>
>>> aminoacids.rtp  cgWater.itp  ffPACE_1.3-c.tdb  ffPACE_1.3.hdb
>>>  ffPACE_1.3-n.tdb
>>> cg216water.gro  ffPACE_1.3.atp  ffPACE_1.3.ddb    ffPACE_1.3.itp
>>>  ffPACE_1.3.rtp
>>>
>>> Compared to the standard forcefields, such as CHARMM and AMBER, there is
>>> no
>>> .doc. I located these files in
>>> /usr/local/gromacs/share/gromacs/top/PACE_1.3.ff.
>>>
>>> When I tried to implement the forcefield with pdb2gmx, I see no sign of
>>> PACE and option -ff returns error too.
>>>
>>> I am new to GROMACS. Would anyone suggest any solution or references that
>>> I
>>> should look into?
>>>
>>>
>> You need a forcefield.doc file that has the force field name so that
>> pdb2gmx can find it.
>>
>> -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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-- 
==================================================

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

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