Can anyone help me out kindly...regarding the previous error msg tht i have got.....
<https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.di...@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.. > > > > <https://mailtrack.io/>Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> > > On Tue, Feb 14, 2017 at 6:56 PM, Мижээ Батсайхан <b.mijidd...@gmail.com> > wrote: > >> > ------------------------------ >> > >> > Message: 6 >> > Date: Tue, 14 Feb 2017 16:11:40 +0530 >> > From: Dilip H N <cy16f01.di...@nitk.edu.in> >> > To: gmx-us...@gromacs.org >> > Subject: Re: [gmx-users] Regarding topology... >> > Message-ID: >> > <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A@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 >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.