On 2010-09-09 18.37, Alan wrote:
Hi there,
when using for example:
pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none
I got in the agQQQ.pdb, things like:
ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00
N
ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00
HE
ATOM 17 2HE2 NGL 1 5.066 7.449 2.048 1.00 0.00
HE
ATOM 18 C NGL 1 5.487 2.636 0.037 1.00 0.00
C
I can not reproduce this. Can you please file a bugzilla and load up the
input pdb file?
Notice the last column, in special the "HE". This is wrong!
For most programmes it's not a issue since they seem to ignore the last
column but this column exist and has a propose.
And there programmes that observe this column, like openbabel. If
converting this pdb to mol2 I got wrong structure since babel thinks I
am dealing with Helium atoms.
In gmx 4.0.x the last column was never printed so never had this problem
before.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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