[gmx-users] Re: atom types, residue info for D-amino acids

Anton Feenstra feenstra at chem.vu.nl
Mon Jun 2 16:16:01 CEST 2003

Hi Regina,

If I understood your messages, you have a two-fold problem:
1) you have a .mol file, which Gromacs (or pdb2gmx) can't read.
2) you don't understand (part of) the output of the prodrg2 server.

But, it also seems that, at least at one point, you also have a .pdb
file of your peptide. What would be the problem of feeding that .pdb file
to pdb2gmx (no need for prodrg) directly? If your .mol file lacks atom
and/or residue name information, you should go back to the program you
used to generate that .mol file (e.g., see if it will write a .pdb file
for you). Then, you are left with the D-chirality which is easily fixed
in the .top file pdb2gmx generates, by either inverting the angle of the
corresponding improper dihedrals (on the Ca), or by swapping two atoms
in each of these impropers. IMHO, it is often preferable to rely on
'manual editing' of in- or output file, in stead of relying on the behavior
of 'graphical editing' tool (e.g. a modeling program). In my experience,
there are too many idiosyncratic oddities in the way they interpret the
input files and/or write the output files (e.g., sorting, re-naming
adding or removing atoms).


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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