VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jun 22 2012 - 23:35:14 CDT

Try "patch SAM B:402" (a subtle difference). Also, you should put the patch statement before any coordinates are loaded or guessed, i.e., right after the segment command. Furthermore, make sure to add a "regenerate angles dihedrals" after patching.

On Jun 22, 2012, at 9:37 AM, flavio seixas wrote:

> 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
>
>