[gmx-users] Regarding topology...
Dilip H N
cy16f01.dilip at nitk.edu.in
Thu Feb 16 06:48:38 CET 2017
Can anyone help me out kindly...regarding the previous error msg tht i have
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On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> Hello.. I have created a ammonia molecule... and i have CGennFF also...
> and thn in the terminal if i type gmx pdb2gmx -f ammonia.pdb -o
> ammonia.gro..and thn i enter for charmm36 force field...
> and thn none for water model since i dnt want water (i just want to
> simulate ammonia)..
> and i am getting again residue AMM1 is not thr i rtp file entry..
> But Justin as u tld tht residue for ammonia is AMM1 and tht is in CGenFF...
> Can u rectify me whr the fault is..??
> below is the screen shot of both the terminal error msg and my pdb file
> with errors..
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> On Tue, Feb 14, 2017 at 6:56 PM, Мижээ Батсайхан <b.mijiddorj at gmail.com>
>> > ------------------------------
>> > Message: 6
>> > Date: Tue, 14 Feb 2017 16:11:40 +0530
>> > From: Dilip H N <cy16f01.dilip at nitk.edu.in>
>> > To: gmx-users at gromacs.org
>> > Subject: Re: [gmx-users] Regarding topology...
>> > Message-ID:
>> > <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A at mail.
>> > gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> > How can i create a mixture of molecules and save it in .pdb format..?
>> > Is there any softwares for tht..?? or any software for pdb generator for
>> > gromacs..??
>> > Can anybody help...??
>> > you can use "gmx insert-molecules" (version 5 or later) for the mixture,
>> it needs pdb and topology files. you can use swissparam and prodrg server
>> etc. for generating topology depending on intended force field.
>> I don't know any special pdb generator for gromacs, because there are many
>> software. what kind of system do you need?
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> With Best Regards,
> Ph.D Student,
> Research Scholar,
> Department of Chemistry,
> National Institute of Technology-Karnataka,
> Surathkal, Mangaluru - 575025.
With Best Regards,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
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