From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Sep 25 2013 - 08:35:14 CDT
are you able to simulate just the organic molecule in a vacuum?
On Wed, Sep 25, 2013 at 9:27 AM, Villalain Boullon, Jose
<jvillalain_at_umh.es>wrote:
> 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,****
>
> ** **
>
> “FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR NG2R51 NG2R51 (ATOMS 22495
> 22495)”****
>
> ** **
>
> 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!.****
>
> ** **
>
> José.****
>
> ** **
>
> ** **
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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