[gmx-users] top file in coarse-grained

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 19 20:34:48 CEST 2009

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.


> 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


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