VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Fri Jun 22 2012 - 09:37:17 CDT

Hi all,

I am trying run a simulation of a protein complex to SAM (S-Adenosylmethionine )

However, for the specific case of SAM, there are CHARMM parameters readily available in the main CHARMM force field distribution.

(PRES SAM in toppar/stream/toppar_prot_na_all.str) to create SAM from ADE as described below:

First of all, the ADE was succesfully generated by psfgen. After this point I was trying to generate SAM:

PRES SAM   1.00        ! Patch for ade to get S-adenosyl-methionine
                        ! ade has to be generated prior to application of
                        ! this patch in a separate patch command
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
DELETE ATOM O5'

GROUP   
ATOM N    NH3    -0.30  !

... AND SO ON

I am using this script to generate psf:

package require psfgen
topology toppar_prot_na_all.str
segment B {pdb ade.pdb}
coordpdb ade.pdb
guesscoord
patch SAM B 402
writepdb sam.pdb
writepsf sam.psf

The resulting error from TKConsole is:

building segment B
reading residues from pdb file ade.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: skipping bond O3'-P at beginning of segment.
Info: skipping conformation C3'-O3'-P-O5' at beginning of segment.
Info: skipping conformation C4'-C3'-O3'-P at beginning of segment.
Info: skipping conformation O3'-O5'-P-O2P at beginning of segment.
Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
Info: segment complete.
reading coordinates from pdb file ade.pdb for segment B
Warning: failed to set coordinate for atom H3T     ADE:402      B
Warning: failed to set coordinate for atom H5T     ADE:402      B
Info: guessing coordinates for 3 atoms (3 non-hydrogen)
Warning: poorly guessed coordinates for 2 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom O1P     ADE:402      B
Warning: poorly guessed coordinate for atom O2P     ADE:402      B
applying patch SAM to 2 residues
ERROR: resid missing from patch target B
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.

Please could someone give-me a suggestion about what I am doing wrong?

Thanks for any help.

Flavio