[gmx-users] Regarding topology...
Dilip H N
cy16f01.dilip at nitk.edu.in
Tue Feb 14 11:41:47 CET 2017
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...??
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On Tue, Feb 7, 2017 at 4:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Those warnings aren't referring to whether a particle is HETATOM or ATOM.
> You haven't followed step 5 here
> http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field
> it
> seems.
>
> Mark
>
> On Tue, Feb 7, 2017 at 10:59 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > 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
> >
> >
> > <https://mailtrack.io/>Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > 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......
> > >
> > >
> > >
> > >
> > > <https://mailtrack.io/>Sent with Mailtrack
> > > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> > >
> > > 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
> > >>
> > >>
> > >>
> > >> <https://mailtrack.io/>Sent with Mailtrack
> > >> <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> > >>
> > >> 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
> > >>>
> > >>>
> > >>>>
> > >>>> Sent with Mailtrack
> > >>>> <https://mailtrack.io/install?source=signature&lang=en&refer
> > >>>> 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...
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> Sent with Mailtrack
> > >>>>> <https://mailtrack.io/install?source=signature&lang=en&refer
> > >>>>> 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!
> > >>>>>>
> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>
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> > >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > or
> > >>>>>> 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
> > >>> /Mailing_Lists/GMX-Users_List before posting!
> > >>>
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> or
> > >>> 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.
> > --
> > 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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> 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.
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