[gmx-users] pdb2gmx and virtual sites

[Justin A. Lemkul]

Ondrej Marsalek wrote:
> 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?
> 

That's the old benchmark set (version 3.0), and has nothing to do with version 
4.0, for which I do not believe there is an actual set of benchmarks.  I was 
merely referring to the described procedure, parameters, and results obtained in 
the GROMACS 4 paper.

-Justin

> 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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> 

-- 
========================================

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

========================================