VMD-L Mailing List

From: Asaf Farhi (asaf.farhi_at_weizmann.ac.il)
Date: Thu Aug 22 2013 - 11:42:14 CDT

________________________________
From: Asaf Farhi
Sent: Thursday, August 22, 2013 7:41 PM
To: owner-vmd-l_at_ks.uiuc.edu
Subject: generation of psf of phenol

Dear all

Hi. I have been trying today to generate the psf of phenol.
I'm using the following inp pdb and pgn files. It seems that something with the pdb is not good.
I have been playing with the pdb so far with no success.
I will appreciate any help.

I got the following message:

psfgen) reading topology file top_phenol.inp

psfgen) duplicate residue key PHEN will be ignored
psfgen) building segment PH
psfgen) reading residues from pdb file phenol2.pdb
psfgen) extracted 0 residues from pdb file
psfgen) Info: generating structure...segment complete.
psfgen) reading coordinates from pdb file phenol2.pdb for segment PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C1* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C2* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C3* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C4* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C5* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom C6* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H1* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H2* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H3* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H4* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H5* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom H6* : PH
psfgen) no residue of segment PH
psfgen) Warning: failed to set coordinate for atom O1* : PH
psfgen) Info: writing pdb file phenol7.pdb
psfgen) Info: pdb file complete.
psfgen) Info: writing psf file phenol7.psf
psfgen) total of 0 atoms
psfgen) total of 0 bonds
psfgen) total of 0 angles
psfgen) total of 0 dihedrals
psfgen) total of 0 impropers
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.

inp file:
RESI PHEN 0.00 ! phenol, adm jr.
GROUP
ATOM CG CA -0.115 !
ATOM HG HP 0.115 ! HD1 HE1
GROUP ! | |
ATOM CD1 CA -0.115 ! CD1--CE1
ATOM HD1 HP 0.115 ! / \
GROUP ! HG--CG CZ--OH
ATOM CD2 CA -0.115 ! \ / \
ATOM HD2 HP 0.115 ! CD2--CE2 HH
GROUP ! | |
ATOM CE1 CA -0.115 ! HD2 HE2
ATOM HE1 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM CZ CA 0.11
ATOM OH OH1 -0.54
ATOM HH H 0.43
BOND CD1 CG CD2 CG CE1 CD1
BOND CE2 CD2 CZ CE1 CZ CE2
BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1
BOND CE2 HE2 CZ OH OH HH
IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000
IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000
IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000
IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000
IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000
IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000
IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000

the following pdb:
ATOM 1 C1* 1 -1.303 0.791 -0.263
ATOM 2 C2* 1 -0.174 1.534 -0.625
ATOM 3 C3* 1 1.100 0.976 -0.496
ATOM 4 C4* 1 1.248 -0.324 -0.003
ATOM 5 C5* 1 0.120 -1.072 0.357
ATOM 6 C6* 1 -1.155 -0.508 0.228
ATOM 7 H1* 1 -2.036 -1.081 0.515
ATOM 8 H2* 1 0.309 -2.477 1.658
ATOM 9 H3* 1 2.244 -0.753 0.099
ATOM 10 H4* 1 1.979 1.557 -0.770
ATOM 11 H5* 1 -0.288 2.554 -0.990
ATOM 12 H6* 1 -2.295 1.229 -0.355
ATOM 13 O1* 1 0.251 -2.426 0.646
CONECT 1 2 6 12
CONECT 1 2 6
CONECT 2 1 3 11
CONECT 2 1
CONECT 3 2 4 10
CONECT 3 4
CONECT 4 3 5 9
CONECT 4 3
CONECT 5 4 6 13
CONECT 5 6
CONECT 6 1 5 7
CONECT 6 1 5
CONECT 7 6
CONECT 8 13
CONECT 9 4pgn
CONECT 10 3
CONECT 11 2
CONECT 12 1
CONECT 13 8 5
END

and the following pgn:
package require psfgen
topology top_phenol.inp
segment PH {pdb phenol2.pdb}
coordpdb phenol2.pdb PH
writepdb phenol7.pdb
writepsf phenol7.psf

Thanks in advance,
Best regards,
Asaf