[gmx-users] topology file for DNA molecule

[Anton Feenstra]

tenghl wrote:

> Hello Andrey,
> 
> Thanks for your suggestion. This time, that error can be avoid. However, it seems O5' can not be recognized.
> Should I change the name of O5' manually? 

Probably yes. For proteins, pdb2gmx has a set of rules to convert common naming
schemes to those used in the Gromacs forcefield(s). For nucleic acids, that hasn't
been done properly yet, mostly because it appears naming in nuc.ac. is much less
standard than in proteins! You'll have to look carefully at your .pdb file and at
the corresponding .rtp building blocks, and decide to which atom from the .rtp
the O5' from your.pdb will match.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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 few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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