From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sat Jun 23 2012 - 14:13:14 CDT

Hi Gumbart,

Thank you for your help. It works very fine!
SAM has a non standard sulphur atom. Web resources were not able to generate parameters for this compond.

Regards,

Flavio

--- On Sat, 6/23/12, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> From: JC Gumbart <gumbart_at_ks.uiuc.edu>
> Subject: Re: vmd-l: patch SAM in psfgen
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>
> Cc: "VMD List" <vmd-l_at_ks.uiuc.edu>
> Date: Saturday, June 23, 2012, 5:35 AM
> 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
> >
> >
>
>
>