Stefano Meliga wrote:
Hello,
I noticed that the command editconf -i structure.gro -o structure.pdb
produce a pdb file in which some atom names are not standard.
In particular the delta carbon on ILE:
"CD ILE" should be "CD1 ILE";
and the oxigens of the C-terminus
"O1" should be "O "
"O2" should be "OXT".
This is particularly annoying when GROMACS' output pdb is then used in
input of other software, e.g. FIRST.
You might want to fix this.
I think "should be" is a matter of perspective. The atoms are named according
to GROMACS convention, and are used consistently within all force field files
(.rtp, .tdb, etc). If you are aware of inconsistencies with other programs, I
would think a few simple find-and-replace commands in a text editor (or
scripting, awk, sed, etc) would solve the problem, without a re-write of
numerous GROMACS files (and code?).
-Justin
Sincerely,
Stefano
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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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