[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field
udaya kiran marelli
kiran.udaya at gmail.com
Mon Jun 20 18:39:09 CEST 2011
Dear Mark Abraham,
Thank you for your support. However, I have edited the N-terminus in -hdb
file so as too include a HN atom for the specific residue and it worked.
regards,
Uday..
On Fri, Jun 17, 2011 at 10:29 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. cyclic peptide on GROMACS compatoble with Charmm (all-atom)
> force field (udaya kiran marelli)
> 2. Re: gmx4.5.4 genion problem: No line with moleculetype 'SOL'
> found (Ye Yang)
> 3. gmx4.5.4 genion problem: No line with moleculetype 'SOL'
> found (chris.neale at utoronto.ca)
> 4. Re: cyclic peptide on GROMACS compatoble with Charmm
> (all-atom) force field (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 17 Jun 2011 17:13:54 +0200
> From: udaya kiran marelli <kiran.udaya at gmail.com>
> Subject: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm
> (all-atom) force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear GROMACS users,
>
> I am trying to construct a cyclic hexa peptide containing all Ala residues.
> During pdb2gmx conversion using the command (pdb2gmx -ff charmm27 -ignh
> -f TESTALA.pdb -o TESTALA.gro -ter) it gave the following error while I am
> demanding the program to give uncharged termini (option : None)
>
> WARNING: atom HN is missing in residue ALA 1 in the pdb file
> You might need to add atom HN to the hydrogen database of residue
> ALA
> in the file ff???.hdb (see the manual)
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pdb2top.c, line: 704
>
> Fatal error:
> There were 1 missing atoms in molecule Protein, if you want to use this
> incomplete topology anyhow, use the option -missing
>
> In the .hdb file the atom HN is defined already. The error is that it is
> removing the #HN# atom from the Ala 1 residue at the cyclization point.
>
> Could you suggest me in getting rid off the problem.
>
>
> yours sincerely
> Uday.
>
> Marelli Udaya Kiran
> C/o. Professor Dr. Horst Kessler
> Institute for Advanced Study
> Department Chemie
> Technische Universität München
> Lichtenbergstrasse 4
> D-85747 Garching, Germany
>
> Tel.: +49-(0)89-289-13760
> Fax: +49-(0)89-289-13210
> email: kiran.udaya at tum.de
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> ------------------------------
>
> Message: 2
> Date: Fri, 17 Jun 2011 13:06:44 -0400
> From: Ye Yang <knightyangpku at gmail.com>
> Subject: Re: [gmx-users] gmx4.5.4 genion problem: No line with
> moleculetype 'SOL' found
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <BANLkTinRa2ff2aBDnWcBbKKX0FTZNWyiKw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you for your suggestions.
> I have checked the topology file with vim, and it looks pefectly, also, the
> only problem happens when I use genion. One thing that might be possible is
> that I use the double precision version of gromacs, because when I solve it
> in water, the written of topology file looks weired(like I showed).
> What do you mean by work-around? You mean just manually change some water
> molecules in topology file and coordinate file into ions? Will the program
> recognize something like CL, NA? Or can I just add ions to the system and
> solve it in water?
>
> Thank you very much
>
> Best
> Wishes
>
> Ye
>
> 2011/6/16 Justin A. Lemkul <jalemkul at vt.edu>
>
> >
> >
> > Ye Yang wrote:
> >
> >> Hi, everyone:
> >> I am a new user of Gromacs, and I am running through the tutorial.
> >> When I am trying to run the ligand-receptor binding tutorial from
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> >> I met some trouble in adding ion.
> >> Each time when I use genion, it shows:
> >>
> >> Will try to add 0 NA ions and 6 CL ions.
> >> Select a continuous group of solvent molecules
> >> Group 0 ( System) has 33046 elements
> >> Group 1 ( Protein) has 1693 elements
> >> Group 2 ( Protein-H) has 1301 elements
> >> Group 3 ( C-alpha) has 163 elements
> >> Group 4 ( Backbone) has 489 elements
> >> Group 5 ( MainChain) has 653 elements
> >> Group 6 ( MainChain+Cb) has 805 elements
> >> Group 7 ( MainChain+H) has 815 elements
> >> Group 8 ( SideChain) has 878 elements
> >> Group 9 ( SideChain-H) has 648 elements
> >> Group 10 ( Prot-Masses) has 1693 elements
> >> Group 11 ( non-Protein) has 31353 elements
> >> Group 12 ( Other) has 15 elements
> >> Group 13 ( JZ4) has 15 elements
> >> Group 14 ( Water) has 31338 elements
> >> Group 15 ( SOL) has 31338 elements
> >> Group 16 ( non-Water) has 1708 elements
> >> Select a group: 15
> >> Selected 15: 'SOL'
> >> Number of (3-atomic) solvent molecules: 10446
> >>
> >> Processing topology
> >>
> >> Back Off! I just backed up temp.top to ./#temp.top.3#
> >>
> >> -------------------------------------------------------
> >> Program genion_d, VERSION 4.5.4
> >> Source code file: gmx_genion.c, line: 285
> >>
> >> Fatal error:
> >> No line with moleculetype 'SOL' found the [ molecules ] section of file
> >> 'topol.top'
> >>
> >>
> > Something doesn't match up here - the command backs up temp.top, but then
> > complains it can't find SOL in topol.top. Either genion is looking at
> the
> > wrong file or your command is somehow wrong.
> >
> >
> > I checked my topology file and it looks fine:
> >> ; Include Position restraint file
> >> #ifdef POSRES
> >> #include "posre.itp"
> >> #endif
> >>
> >> ; Include water topology
> >> #include "gromos43a1.ff/spc.itp"
> >>
> >> ; Include ligand topoloty
> >> #include "drg.itp"
> >> #ifdef POSRES_WATER
> >> ; Position restraint for each water oxygen
> >> [ position_restraints ]
> >> ; i funct fcx fcy fcz
> >> 1 1 1000 1000 1000
> >> #endif
> >>
> >> ; Include topology for ions
> >> #include "gromos43a1.ff/ions.itp"
> >>
> >> [ system ]
> >> ; Name
> >>
> >> Protein
> >> [ molecules ]
> >> ; Compound #mols
> >> Protein_chain_A 1
> >> JZ4 1 SOL 10446
> >>
> >> One thing that might happen is in the genion source file, I read
> through
> >> it, and the problem either happens in loading the line to buf2, or in
> the
> >> gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 aftermath.
> >>
> >> The other thing I tried is to remove the ligand JZ4 part in both
> topology
> >> and coordinates file, and in this case, it works perfectly for adding
> ion.
> >> But in this way, I do not know how to insert my ligand into the system
> since
> >> it might collide with solvent.
> >>
> >>
> > If removal of the JZ4 line relieves the problem, perhaps there's a
> problem
> > with that line, i.e. the line ending? What type of system are you using?
> > Sometimes Windows line endings cause problems. Always use a plain text
> > editor and use dos2unix to process text files if you're on Windows.
> >
> > Otherwise, the work-around is to not have genion work on the topology.
> > Make the corrections yourself. Simple addition of ions and subtraction
> of
> > water molecules is trivial.
> >
> > -Justin
> >
> >
> > Can someone help me with this problem?
> >>
> >> Thank you all very much.
> >>
> >> Ye Yang
> >>
> >>
> >>
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> >
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> > Please don't post (un)subscribe requests to the list. Use the www
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> ------------------------------
>
> Message: 3
> Date: Fri, 17 Jun 2011 16:04:54 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] gmx4.5.4 genion problem: No line with
> moleculetype 'SOL' found
> To: gmx-users at gromacs.org
> Message-ID: <20110617160454.y27k51qt1k4oc848 at webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> For the quick fix:
>
> 1. run genion on your topology that does work. Look at this to see the
> format of the ion atom and residue names
>
> 2. Pick a few waters in the structure containing the ligand and
> replace the OW by the ion and remove the hydrogens, then fix the
> number of atoms on the second line of the file and run editconf on the
> file.
>
> ** But I wouldn't be satisfied with that if I were you. there is some
> problem here that you should uncover now before you move farther.
>
> Show us your commands exactly (copy and paste) and perhaps we can help
> more.
>
> As a side note: your topology that you presented is going to cause
> you problems if you try to put position restraints on the water, as it
> is incorrectly ordered:
>
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
>
> ; Include ligand topoloty
> #include "drg.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
>
> -- original message --
>
> Thank you for your suggestions.
> I have checked the topology file with vim, and it looks pefectly, also, the
> only problem happens when I use genion. One thing that might be possible is
> that I use the double precision version of gromacs, because when I solve it
> in water, the written of topology file looks weired(like I showed).
> What do you mean by work-around? You mean just manually change some water
> molecules in topology file and coordinate file into ions? Will the program
> recognize something like CL, NA? Or can I just add ions to the system and
> solve it in water?
>
> Thank you very much
>
> Best
> Wishes
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 18 Jun 2011 06:29:39 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] cyclic peptide on GROMACS compatoble with
> Charmm (all-atom) force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFBB933.2010806 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 18/06/2011 1:13 AM, udaya kiran marelli wrote:
> > Dear GROMACS users,
> >
> > I am trying to construct a cyclic hexa peptide containing all Ala
> > residues. During pdb2gmx conversion using the command (pdb2gmx -ff
> > charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the
> > following error while I am demanding the program to give uncharged
> > termini (option : None)
> >
> > WARNING: atom HN is missing in residue ALA 1 in the pdb file
> > You might need to add atom HN to the hydrogen database of
> > residue ALA
> > in the file ff???.hdb (see the manual)
>
> With -ignh you told it to strip away all the H atoms, and that requires
> that pdb2gmx knows how to rebuild them (or doesn't need to know).
>
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 4.0.5
> > Source code file: pdb2top.c, line: 704
> >
> > Fatal error:
> > There were 1 missing atoms in molecule Protein, if you want to use
> > this incomplete topology anyhow, use the option -missing
> >
> > In the .hdb file the atom HN is defined already. The error is that it
> > is removing the #HN# atom from the Ala 1 residue at the cyclization
> point.
>
> If you mean that the the cyclization is achieved with a peptide bond
> from "N-terminal" N to "C-terminal" C, you will have to use the
> specbond.dat mechanism to achieve that. See chapter 5.
>
> The problem arises because HN is defined in the .hdb in terms of C in
> the preceding residue, which is not applicable in your case, because
> there is not a regular peptide bond.
>
> Rather than the "brute force" -ignh mechanism, there may be a better
> approach (like removing particular offending hydrogen atoms from your
> input coordinate file) that doesn't require pdb2gmx to need to know how
> to rebuild HN.
>
> Mark
>
> > Could you suggest me in getting rid off the problem.
> >
> >
> > yours sincerely
> > Uday.
> >
> > Marelli Udaya Kiran
> > C/o. Professor Dr. Horst Kessler
> > Institute for Advanced Study
> > Department Chemie
> > Technische Universität München
> > Lichtenbergstrasse 4
> > D-85747 Garching, Germany
> >
> > Tel.: +49-(0)89-289-13760 <tel:%2B49-%280%2989-289-13760>
> > Fax: +49-(0)89-289-13210 <tel:%2B49-%280%2989-289-13210>
> > email: kiran.udaya at tum.de <mailto:kiran.udaya at tum.de>
> >
>
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