[gmx-users] Regarding topology...
Mark Abraham
mark.j.abraham at gmail.com
Tue Feb 7 11:44:15 CET 2017
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@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@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@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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> 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!
> >>>
> >>> * 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-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
>
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