Re: problem:psfgen- not unique coordinates

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon Feb 09 2004 - 20:05:30 CST

You were on the right track, Satyavani. Psfgen is trying to patch the
ethanol with an N- and C- terminus as if it were a protein. The "dummy
atoms" at the origin were those patch atoms. The following fix to your
script eliminates the problem.

resetpsf
package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U1 {pdb protein.pdb}
coordpdb protein.pdb U1
segment U2 {
  pdb alcohol.pdb
  first none
  last none
  }
coordpdb alcohol.pdb U2
guesscoord
writepdb pro-alc.pdb
writepsf pro-alc.psf
exit

-Tim

On Mon, 9 Feb 2004, Satyavani Vemparala wrote:

>
> Hello:
>
> I am new to NAMD and i had a problem trying to guess coordinates of
> hydrogens and generating pdb and psf files from two different segments of
> protein & alcohol atoms.
>
> I have a protein and an alcohol molecule, and i made two seperate pdb
> files for these. Then i modified the topology file to include the bonding
> and residue information of the alcohol. Now when i use the psf gen to
> guess coordinates and write combined pdb and psf files, it does it but
> also at the end of the protein, includes some dummy atoms all with
> coordinates at the origin!
>
> Has it something to do with the lines:
> DECL -CA
> DECL -C
> DECL -O
> DECL +N
> DECL +HN
> DECL +CA
> DEFA FIRS NTER LAST CTER
>
> in the CHRMM topology files? is the PSF generatoe expecting that the
> second segment is also a protein and trying to attach?
>
> Has anybody else faced this issue, and can anyone suggest a solution to
> that?
>
> my script to generate combined PSF & PDB files:
>
> package require psfgen
> topology top_all27_prot_lipid.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment U1 {pdb protein.pdb}
> coordpdb protein.pdb U1
> segment U2 {pdb alcohol.pdb}
> coordpdb alcohol.pdb U2
> guesscoord
> writepdb pro-alc.pdb
> writepsf pro-alc.psf
> ------------------------
> MODIFICATION IN TOPOLOGY FILES:
> -------------------------------
>
> !-----------------ALCOHOLS-------------------------
> ! ETHANOL
> ! =====================
> ! HA1 HB1
> ! | |
> ! HA3-CA1-CB1-OL1-HL1
> ! | |
> ! HA2 HB2
> !
> RESI EOH 0.00
> GROUP
> ATOM CA1 CT3 -0.27
> ATOM HA1 HA 0.09
> ATOM HA2 HA 0.09
> ATOM HA3 HA 0.09
> ATOM CB1 CT2 0.05
> ATOM HB1 HA 0.09
> ATOM HB2 HA 0.09
> ATOM OL1 OH1 -0.66
> ATOM HO1 H 0.43
>
> BOND CA1 HA1 CA1 HA2 CA1 HA3 CA1 CB1
> BOND CB1 HB1 CB1 HB2
> BOND OL1 CB1
> BOND OL1 HO1
>
> AUTO ANGLES DIHE
>
>
> Thanks
> Vani
>
>
>

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