[gmx-users] Regarding topology...

Dilip H N cy16f01.dilip at nitk.edu.in
Tue Feb 7 10:59:25 CET 2017 

I am getting this error after giving the  command gmx pdb2gmx -f
ammonia,pdb -o ammonia.gro
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, Feb 7, 2017 at 3:20 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> 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/groma
>> cs/top/charmm36-nov2016.ff/merged.hdb
>> Opening force field file /usr/local/gromacs/share/groma
>> cs/top/charmm36-nov2016.ff/merged.n.tdb
>> Opening force field file /usr/local/gromacs/share/groma
>> cs/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/groma
>> cs/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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>>>> ral=cy16f01.dilip at 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...
>>>>>
>>>>>
>>>>>
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>>>>> ral=cy16f01.dilip at 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
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>>>>>>
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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
>>>
>>> * 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.
>>
>
>
>
> --
> 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.

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