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 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<<
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