[gmx-users] Regarding topology...

[Dilip H N]

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
spce.
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.
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> -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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-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.