[gmx-users] H2 topology

[011013021-Jyotsna]

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

  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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