[gmx-users] top file in coarse-grained

[Justin A. Lemkul]

Francesco Pietra wrote:
> Hi Justin:
> Could you please indicate the location of such scripts?
> 

They're on the MARTINI website, but given the further description of your 
system, they won't solve your problem.  What I was referring to were scripts to 
build protein topologies.  They won't help in subsequent steps of building the 
system.

> I have no trouble (in generating the .tpr file) with protein partly
> embedded in a double layer, by counting graphically the lipid residues
> and W residues remaining after creating the hole for the protein pore
> region.
> 
> My trouble is with water blocks added to the parts of protein emerging
> from the double layer. Operating as above, no match .gro/.top is
> obtained.
> 

So the problem is in counting the water molecules?  It's fairly simple:

grep W structure.gro | wc -l

Then just update the topology accordingly.  From your description, though, it 
sounds like you have a method for counting the W particles, so perhaps I don't 
understand what the problem is.  To get additional help, it would be useful to 
see what commands you're using to create your system.

> On the other hand, it seems that in GROMACS there is no such
> possibilty as with AMBER's LEAP to solvate EXTERNALLY a system. Which
> was what I used with all-atoms in AMBER.
> 

Not true.  That's what genbox is for.  As for considerations of the difficulties 
of a membrane system, see here:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

You just need an appropriate solvent box, which is provided by the MARTINI folks.

-Justin

> thanks
> francesco
> 
> On Mon, Oct 19, 2009 at 8:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Francesco Pietra wrote:
>>> Hi:
>>>
>>> As I meet recurring problems in coarse-grained of the top file not
>>> matching the number of coordinates in coordinate file, is there any
>>> way to get the top file automatically like in all-atoms? Editing the
>>> top file to this regard proved difficult in my hands.
>>>
>> I'm assuming you're still using MARTINI?  They provide scripts that will
>> write the topology for you.  If you're using those and still having trouble,
>> be aware that those scripts are not as intelligent as pdb2gmx.  They will
>> write the topology regardless of whether or not all the atoms are present in
>> your starting structure.  That is, if you tell it there is an ARG residue,
>> but the original .pdb file has missing atoms in that residue, the MARTINI
>> scripts will happily write a topology for an intact residue, but you will
>> still be missing atoms in the structure.  At least one other user struggled
>> with this issue not too long ago.
>>
>> -Justin
>>
>>> thanks
>>> francesco pietra
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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

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