Organic molecule and membrane. NAMD gives fatal error:

From: Villalain Boullon, Jose (
Date: Wed Sep 25 2013 - 08:27:59 CDT

Dear NAMD users,


Sorry, I have been unable to find the possible solution/s in the mailing list to the problem I have when using NAMD.


I want to work with a small organic molecule (built using Avogadro) inserted into a homogeneous membrane. It has been difficult to obtain the psf file for the organic molecule. In the end I have obtained it using PDB Reader (using both pdb and mol files and the Charmm General Force Field). Obtaining the psf and pdb files for the membrane is straightforward using Charmm-Gui.


In order to combine both the molecule and the membrane, I have used VMD (using readpsf and coordpdb and then writepsf and writepdb). I have used the xplor_ext psf files (it was not possible using the other psf files).


However, using the corresponding parameter files, whenever I begin NAMD the following error appears,




Sometimes is NG2R51, sometimes CG2R51, etc.


Moreover, several warnings appear in the log file (duplicate bond entry, duplicate angle entry, duplicate dihedral entry, .....)


I have checked the topology and parameter files and as far as I know, and I found no problem with them. However, I suppose that the problem relies in either the topology or the parameter files or both (I have tried also AutoPSF builder within VMD but without any success, since many errors appear).


Thanks a lot for any suggestions!.





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