[gmx-users] Regarding topology...

[Mark Abraham]

Hi,

What errors? I already helped you with some. The list can't accept
attachments, so we can't see a screenshot. Copy and paste.

Mark

On Thu, 16 Feb 2017 06:49 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Can anyone help me out kindly...regarding the previous error msg tht i have
> got.....
>
>
>
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>
> On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > 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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> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
> >
> > On Tue, Feb 14, 2017 at 6:56 PM, Мижээ Батсайхан <b.mijiddorj at gmail.com>
> > wrote:
> >
> >> > ------------------------------
> >> >
> >> > 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?
> >>
> >> Regards,
> >> Miji
> >> --
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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.
> --
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