[gmx-users] Regarding topology...

Tue Feb 7 10:50:43 CET 2017

What will happen if HETATM or ATOM is stated for atom type in 1st column..
I am getting different errors for having HETATM and ATOM......

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On Tue, Feb 7, 2017 at 3:18 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

>
> I have created 16 molecules of ammonia from avogadro software, and below
> is the .pdb file of ammonia...
> Here is my ammonia.pdb file
> I have Charmm force field...
> Than i gave the command gmx pdb2gmx -f ammonia,pdb -o ammonia.gro
> Got the force field, selected charmm36 force field, and entered none for
> water model..
> After that i am getting the error as...
> Sorting it all out...
> Opening force field file /usr/local/gromacs/share/
> gromacs/top/charmm36-nov2016.ff/merged.hdb
> Opening force field file /usr/local/gromacs/share/
> gromacs/top/charmm36-nov2016.ff/merged.n.tdb
> Opening force field file /usr/local/gromacs/share/
> gromacs/top/charmm36-nov2016.ff/merged.c.tdb
> Processing chain 1 (1024 atoms, 256 residues)
> Warning: Starting residue AMM10 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM10 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM10 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM10 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM10 in chain not identified as Protein/RNA/DNA.
> More than 5 unidentified residues at start of chain - disabling further
> warnings.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Opening force field file /usr/local/gromacs/share/
> gromacs/top/charmm36-nov2016.ff/merged.arn
>
>
>
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>
> On Tue, Jan 17, 2017 at 6:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>>
>>>
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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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
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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.