----- Original Message ----- From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu> Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > Dear David, > > Thanks for your reply. From your reply, I get the > impression that the bond length of my hydrogen molecule gets > adjusted duing minimization of the whole system ( protien+water+ > inserted hydrogen molecule). But the issue impending is the > insertion of the hydrogen molecule itself into the protein+water > box created in previous step. For insertion/addition of hydrogen > molecules I used the command: > > genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top ci > h2.gro nmol 100 What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when there's no water, and then solvate *afterwards*. Or, generate solvent, and get a list of 100 random numbers in the right range, manually delete those water molecules to create interstices, update your [molecules] section, then use genconf -ci and equilibrate carefully to fix the density. Or, generate solvent for a box somewhat smaller than the one you want, use editconf -scale to scale the coordinates up to create interstices, use genconf -ci and then minimize really gently to fix all the bond lengths, and equilibrate carefully to fix the density. Mark > It reports to me the inability to add any of the hydrogen > molecules, ie it adds 0 molecules out of 100 requested. > ###########error######################## > Reading molecule configuration > Gallium Rubidium Oxygen Manganese Argon Carbon Silicon > Containing 3 atoms in 1 residue > Initialising van der waals distances... > Try 999 > Added 0 molecules (out of 100 requested) of H2 > Writing generated configuration to 2frv.solv.gro > > Back Off! I just backed up 2frv.solv.gro to ./#2frv.solv.gro.1# > PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE > > Output configuration contains 8340 atoms in 977 residues > Volume : 1299.08 (nm^3) > Density : 143.043 (g/l) > Number of SOL molecules: 186 > > Processing topology > Removing line #40 'SOL 39308' from topology file (2frv.top) > ####################error end############### > How do i rectify this problem? > I suspect the problem is due to the bond length of the > hydrogen molecule that I created with 1.66A distance ( as > described in my previous post) and the fact that the gap between > the solvent molecules (in my case , water) is not big enough to > accomodate the H2 molecules(as I had used the pdb of CO2 and > replaced each O with an H and C atom with dummy atom.). So could > you please help me figure out any tool that helps in adjusting > the bond length of my hydrogen molecule in pdb to the desired > length of 0.7A. > > Or as you said is it possible to minize a single molecule using > md_run program, as I encountered certain problems in doing so . > > Sorry for the lengthy mail. > > Thank you , > Jyotsna > > > > > > > On Wed, 03 Feb 2010 09:30:21 +0100 > David van der Spoel <sp...@xray.bmc.uu.se> wrote: > >*This message was transferred with a trial version of > CommuniGate(r) Pro* > >On 2/3/10 7:52 AM, 011013021-Jyotsna wrote: > >> > >>Dear Justin , > >> > >>Thank you very much for your help. > >>To create a linear H2 molecule with a dummy atom in the center is > >>proving to be quite a difficult task. > >>Hence , I created a pdb file of CO2 using Cerius(2) , and > replaced the > >>atoms in the pdb file with 2 H atoms and a dummy atom.(since > CO2 is a > >>three atom , linear system i.e the two O atoms replaced by two > H atoms > >>and the C atom by the dummy) > >>The problem is the bond distance. For CO2 , it is 1.66 A but I > need the > >>distance for H2 to be only 0.7 A as per the literature I am > following.>>By replacing the atoms in the pdb file , there is a > problem regarding > >>distance since the coordinates of the pdb also point towards > 1.6 A. > >>I would be very grateful if you could tell me how I can build > a PDB for > >>H2 with dummy atom with the right distance. > >> > >>Thank You, > >>Jyotsna > >Doesn't matter if the pdb is wrong initially, you just do an > energy minimization. What is important is (put in exact bond length): > > > >[ bonds ] > >1 2 1 0.74 500000 > > > >[ vsites2 ] > >3 1 2 1 0.5 > > > > > > > >-- > >David van der Spoel, Ph.D., Professor of Biology > >Dept. of Cell & Molec. Biol., Uppsala University. > >Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: > +4618511755.>sp...@xray.bmc.uu.se sp...@gromacs.org > http://folding.bmc.uu.se>-- > >gmx-users mailing list gmx-users@gromacs.org > >http://lists.gromacs.org/mailman/listinfo/gmx-users > >Please search the archive at http://www.gromacs.org/search > before posting! > >Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? 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