[gmx-users] Regarding topology...

[Justin Lemkul]

On 1/17/17 12:23 AM, Dilip H N wrote:
> 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....
>

I provided you the link to where you can get the necessary force field, but 
apparently you didn't actually get those files.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-January/110488.html

-Justin

>
>
>  Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
>
> 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...
>>
>>
>>
>>  Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
>>
>> 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.
>>
>
>
>

-- 
==================================================

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

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