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, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 ([email protected]) > 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 <[email protected]> > Subject: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm > (all-atom) force field > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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: [email protected] > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110617/2685133e/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 17 Jun 2011 13:06:44 -0400 > From: Ye Yang <[email protected]> > Subject: Re: [gmx-users] gmx4.5.4 genion problem: No line with > moleculetype 'SOL' found > To: [email protected], Discussion list for GROMACS users > <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > > > > > > > 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 [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110617/213fe84e/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Fri, 17 Jun 2011 16:04:54 -0400 > From: [email protected] > Subject: [gmx-users] gmx4.5.4 genion problem: No line with > moleculetype 'SOL' found > To: [email protected] > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: Re: [gmx-users] cyclic peptide on GROMACS compatoble with > Charmm (all-atom) force field > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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: [email protected] <mailto:[email protected]> > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110618/37b1e0d9/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 86, Issue 110 > ****************************************** >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
