VMD-L Mailing List

From: ABEL Stephane (Stephane.ABEL_at_cea.fr)
Date: Mon Aug 27 2018 - 10:45:37 CDT

I was able to resolve my problem myself by loading only the *.prm file of the ligand in the "associated Parameter files"
________________________________________
De : owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] de la part de ABEL Stephane
Envoyé : lundi 27 août 2018 15:48
À : vmd-l_at_ks.uiuc.edu
Objet : [PROVENANCE INTERNET] vmd-l: truncated atom types with fftk v.1.93

Hi everybody,

I am using fftk to optimize a ligand. The initial (guessed) parameters were obtained with CHARMM-GUI with a mol2 and pdb obtained from ParamChem. My problem is that during the the first step ("identify the missing parameters") the name of the each atom type is truncated and contains only 4 strings instead 6 or more (for instance CG2R67 instead of CG2R67). I use as input the

- PSF file : step1_pdbreader.xplor_ext.psf
- PDB file : step1_pdbreader.pdb

When I press the "Analysis" button, I obtained the list of the atom types involved in the bonds, angles, etc. with only 4 characters instead of 6 or more as reported in the "step1_pdbreader.xplor_ext.psf" file. Same problem is I save the par file,

I do not know what is wrong.

Can you help me ?

Thanks

Stéphane