[gmx-users] top file in coarse-grained
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 19 21:44:45 CEST 2009
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
> 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
> 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
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:
You just need an appropriate solvent box, which is provided by the MARTINI folks.
> On Mon, Oct 19, 2009 at 8:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Francesco Pietra wrote:
>>> 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.
>>> francesco pietra
>>> gmx-users mailing list gmx-users at gromacs.org
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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
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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