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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