[gmx-users] pdb2gmx and virtual sites

[Ondrej Marsalek]

I thought that this was needed to convert the hydrogens to virtual
sites, based on reading section 6.5 of the manual and some other
things. Is this not correct?

Ondrej


On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> Dear GROMACS users,
>>
>> I would like to substitute hydrogens in a protein with virtual sites
>> to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
>> several other places. So far, I have not found an example or a
>> tutorial that would involve this, so I want to create a
>> straightforward example. I have taken the 2KO3 structure from the PDB
>> and went through this sequence of commands:
>>
>> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
>> -vsite hydrogens -ignh
>> editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
>> genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro
>> grompp
>>
>> I also provided a pretty standard grompp.mdp, that contains
>> "constraints = h-angles". I get the following error:
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.5
>> Source code file: vsite_parm.c, line: 779
>>
>> Fatal error:
>> Automatic parameter generation not supported for Virtual site 3 atom 4
>> for this bonding configuration
>> -------------------------------------------------------
>>
>> I am not sure what the problem is. I would appreciate and help on the
>> use of this feature, pointers to resources, or a working example.
>> Reading the manual and searching did not help as much as I would like.
>>
>
> Have you tried specifying either "all-bonds" or "h-bonds" for constraints?
>  I think "all-bonds" is the most commonly-used option.  Any specific reason
> for using "h-angles"?
>
> -Justin
>
>> Thanks,
>> Ondrej
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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