From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 11 2005 - 11:54:42 CDT
All I can see offhand is a typo towards the end, where you use GTPP
once for the segment and GTPA in the next line.
You can also run these commands individually in the tkcon window; that
might help you find out where something is going wrong.
On Oct 10, 2005, at 6:15 PM, Shirley Li wrote:
> Dear NAMD experts,
>
> I have two questions about psfgen as follows:
>
> 1) The protein has two chains, and it contains GTP. I
> was using psfgen by typing:
> "vmd -dispdev text -e psfgen". While I got warning
> messages that it failed to set coord. for any atom.
> As the result, both the output file "out.pdb" and
> "out.psf" are empty. The script is attached below,
> which is the copy of the one in NAMD website with some
> changes. Could someone please help me out?
>
> 2) Besides, since the terminal residues on both chains
> need to be terminated with ACE/CT3 residues, I wonder
> if it works in the way I set in the psfgen script.
>
> ---------------- psfgen ----------
> package require psfgen
> topology ./top_all27_prot_na_gtp_gdp.inp
> #pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> segment ALPH {
> pdb protein-ALPH.pdb
> first ACE
> last CT3
> }
> coordpdb protein-ALPH.pdb ALPH
> segment BETA {
> pdb protein-BETA.pdb
> first ACE
> last CT3
> }
> coordpdb protein-BETA.pdb BETA
> segment GTPP { pdb protein-GTP.pdb }
> coordpdb protein-GTP.pdb GTPA
> guesscoord
> writepsf out.psf
> writepdb out.pdb
> exit
>
> ----------------------
>
>
>
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