[gmx-users] pdb2gmx and virtual sites

[Ondrej Marsalek]

On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> 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?
>>
>
> I don't believe constraining angles is necessary.  The manual only refers to
> fixed bond lengths.  If you're looking for an example to follow, I would
> suggest running the lysozyme benchmark described in the GROMACS 4 paper;

OK, so now I am mildly confused. I have downloaded the benchmarks pack
(gmxbench-3.0.tar.gz) from the GMX website. The pme.mdp file for
lysozyme indeed says "constraints = all-bonds". On the other hand, the
topology contains virtual sites in the list of atoms, but there are no
[virtual_site?] sections. And the timestep is 4 fs. Could someone
please help me clarify this?

Thanks,
Ondrej


> the
> parameters used are nicely detailed.  I got reasonable results using
> "constraints = all-bonds," but if that is not correct, perhaps someone else
> can comment.
>
> -Justin
>
>> 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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>>
>
> --
> ========================================
>
> 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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