[gmx-users] Regarding topology...
Dilip H N
cy16f01.dilip at nitk.edu.in
Tue Jan 17 05:25:53 CET 2017
Thank you Justin...
1] I have created an Ammonia molecule from Avogadro software...and saved it
in .pdb file format...
2] Than gave the command gmx pdb2gmx -f ammonia.pdb -o ammonia.gro
3] There im not getting the CGenFF force field/r CHARMM36 port..., my
gromacs version is 5.0.7.., How to get/install this force field..?
4] I just ant to simulate ammonia .. and i dnt want water, so i have not
give -spce command @ the end as - gmx pdb2gmx -f ammonia.pdb -o
ammonia.gro instead of gmx pdb2gmx -f ammonia.pdb -o ammonia.gro -water
Hope this is right command...
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On Tue, Jan 17, 2017 at 12:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/16/17 2:44 AM, Dilip H N wrote:
>> My questions are..
>> 1] how to create a topology file for ammonia.??
>> 2] how to create a force field for ammonia, what is the residue name for
>> ammonia in .pdb file.??
>> 3] Why ammonia.itp is not there in gromacs..??
>> 4] Which force field to choose for ammonia..??
> The CHARMM General Force Field (CGenFF) supports ammonia. Its residue
> name is AMM1 and it is in our CHARMM36 port for GROMACS. Use pdb2gmx on a
> suitably named coordinate file and you've got your topology.
> 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
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With Best Regards,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
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