VMD-L Mailing List

From: ABEL Stephane (Stephane.ABEL_at_cea.fr)
Date: Mon Aug 27 2018 - 08:48:47 CDT

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

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Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
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