[gmx-users] Regarding topology...

[Dilip H N]

when the command is given   gmx pdb2gmx -f ammonia.pdb -o ammonia.gro  , it
says as fllows...
Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

But i am not getting CHARMM General Force Field (CGenFF) / CHARMM36 port...
what is the solution...?? my Gromacs version is 5.0.7....



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On Tue, Jan 17, 2017 at 9:55 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> 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.
>



-- 
With Best Regards,

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