VMD-L Mailing List

From: lucie huynh (luciehuynh_at_gmail.com)
Date: Tue Mar 27 2007 - 09:54:08 CDT

Hi everybody,

I'd like to build a water box for a protein. I have already a psf file that
I buid from Charmm but it seems that VMD could'nt read it.
> package require solvate
1.2
> solvate cyp4.psf cyp4.pdb -t 10 -o cyp5_wb
reading structure from psf file cyp4.psf
error reading atoms
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

So I'm trying to generate a psf file of my protein with ACE patch at N-term
and CT2 patch at C-term.
Here are what I entered in Tk console and his messages:

>package require psfgen
>topology top_all22_prot2.inp
>pdbalias residue HIS HSD
>pdbalias atom ILE CD1 CD
>pdbalias atom HSD H HN
>pdbalias atom HIS H HN

>segment CYP {pdb cyp3a4_noheme_nopatch.pdb}
building segment CYP
reading residues from pdb file cyp3a4_noheme_nopatch.pdb
extracted 470 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.

>patch ACE CYP:28
applying patch ACE to 1 residues
no atom HN in residue HSD:28 of segment CYP
Warning: add improper failed in patch ACE
no atom HN in residue HSD:28 of segment CYP
Warning: add conformation failed in patch ACE

>patch CT2 CYP:499
applying patch CT2 to 1 residues

It seems there's a problem in the recognition of the atom HN of the HSD:28
which is the first residu in my pdb file.
The pdb I obtain through the psfgen has the patch ACE at the N-term but VMD
has also added 3 H to the N-term:

ATOM 1 CAY HSD 28 -29.922 7.380 -12.479 0.00 0.00
CYP
ATOM 2 HY1 HSD 28 -30.569 8.125 -12.318 0.00 0.00
CYP
ATOM 3 HY2 HSD 28 -29.127 7.483 -11.882 0.00 0.00
CYP
ATOM 4 HY3 HSD 28 -30.365 6.500 -12.308 0.00 0.00
CYP
ATOM 5 CY HSD 28 -29.620 7.412 -13.432 0.00 0.00
CYP
ATOM 6 OY HSD 28 -28.973 6.667 -13.594 0.00 0.00 CYP

ATOM 7 N HSD 28 -30.070 8.178 -13.891 1.00 0.00
CYP
ATOM 8 HT1 HSD 28 -31.062 8.054 -13.868 0.00 0.00
CYP
ATOM 9 HT2 HSD 28 -29.824 9.037 -13.442 0.00 0.00
CYP
ATOM 10 HT3 HSD 28 -29.620 7.412 -13.432 0.00 0.00
CYP
ATOM 11 CA HSD 28 -29.618 8.226 -15.315 1.00 0.00
CYP
ATOM 12 HA HSD 28 -29.861 7.312 -15.856 1.00 0.00
CYP
ATOM 13 ND1 HSD 28 -32.203 7.912 -17.008 1.00 0.00
CYP

I have the same problem at the C-term: patch CT2, plus OT1, OT2:

ATOM 7645 C THR 499 -23.671 -60.575 -22.449 1.00 0.00
CYP
ATOM 7646 O THR 499 -22.471 -60.357 -22.741 1.00 0.00
CYP
ATOM 7647 NT THR 499 -24.122 -61.292 -21.917 0.00 0.00
CYP
ATOM 7648 HT1 THR 499 -23.430 -61.930 -21.578 0.00 0.00
CYP
ATOM 7649 HT2 THR 499 -25.107 -61.121 -21.910 0.00 0.00
CYP
ATOM 7650 OT1 THR 499 -22.772 -60.140 -22.504 0.00 0.00
CYP
ATOM 7651 OT2 THR 499 -24.119 -61.425 -22.173 0.00 0.00
CYP
ATOM 7652 N THR 499 -24.109 -58.336 -23.384 1.00 0.00
CYP
ATOM 7653 HN THR 499 -23.578 -58.399 -24.229 0.00 0.00 CYP

I tried to add patch NONE CYP:28/499 before adding patch ACE and CT2, but
the termini are still NH3 and COO.
It seems that VMD systematically add the H3 and the OO.

Could anyone help me to solve this problem?
Maybe it comes from the error when building the segment CYP:

>segment CYP {pdb cyp3a4_noheme_nopatch.pdb}
building segment CYP
reading residues from pdb file cyp3a4_noheme_nopatch.pdb
extracted 470 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.

Thanks a lot for your help or any suggestion that will help!

Lucie Huynh