[gmx-users] H2 topology

[David van der Spoel]

On 2/3/10 10:18 AM, 011013021-Jyotsna wrote:
>
> 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 .
Actually for a single molecule you can just do it in a text editor. Set 
the first coordinate to 0 and the second to 0.074 nm.

If genbox doesn't insert it could be because there is no space in the box.

>
> 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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>


-- 
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