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 <jalem...@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
========================================
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