[gmx-users] top file in coarse-grained

[Francesco Pietra]

Hi Justin:
Could you please indicate the location of such scripts?

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.

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.

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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