[gmx-developers] Atom names in ffG53a6.rtp

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 15 14:26:02 CEST 2009

Alexey Shvetsov wrote:
> Its not a good idea if i want to split pdb to chains or something else.

You could simply change the atom names in the .rtp file to something that 
actually fits, for those atoms that are too long.


> 2009/7/15 Mark Abraham <Mark.Abraham at anu.edu.au>:
>> Alexey Shvetsov wrote:
>>> Hi all!
>>> Seems there is some problem with atom names for some rtp entrys in
>>> ffG53a6.rtp (for example for ATP) because atom names in pdb file
>>> cannot be longer then 4 symbols while ATP rtp entry has some names
>>> which are 5 symbols long
>>> so in this case i cannot create toplogy from PDB file with pdb2gmx.
>> Convert the .pdb file to some other more accommodating format (.gro?) with
>> editconf -f in.pdb -o out.gro, before using it as input to pdb2gmx.
>> Mark
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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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