[gmx-users] H2 topology

[Mark Abraham]

----- Original Message -----
From: 011013021-Jyotsna <011013021 at bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users <gmx-users at 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 <spoel at 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.>spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se>-- 
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