Topic Options
#993 - 02/27/04 06:21 PM compatibility of CHARMM
firer Offline
Forum Member

Registered: 11/11/03
Posts: 54
I have lots of script, which worked pretty well for c27b4 version of CHARMM. but, these scripts always get complain if c30b1 version of CHARMM is used.
For example, I got following the warning messages from c30b1,

-----------------------------------------------------------------------
** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= SC3 INPUT= LYS

** WARNING ** For atom in coordinate file, the corresponding residue in the PSF lacks that atom:
INDEX= 4225 IRES= 1 RESID=1 RES=LYS ATOM=N
-----------------------------------------------------------------------

actually, I checked residue type, residue number, segid, segname for both the psf and pdb files. They all matched.

----------
pdb file
----------
ATOM 4224 H21 SC3 132 30.203 -22.606 5.220 1.00 0.00 P132
ATOM 4225 N LYS 1 4.626 8.985 23.689 1.00 0.00 7LYZ
ATOM 4226 HT1 LYS 1 5.652 9.059 23.474 1.00 0.00 7LYZ

---------
psf file
---------
4224 P132 132 SC3 H21 3 0.900000E-01 1.00800 0
4225 7LYZ 1 LYS N 56 -0.300000 14.0070 0
4226 7LYZ 1 LYS HT1 2 0.330000 1.00800 0


any hint for this? I almost crazy for this. It seems that new version of charmm can not read the coordinate from pdb file due to mismatch. But, I did not find any mismatch residue type on pdb and psf file. Again, the same script did not encounter any problem for the old version of charmm.

Jay

Top
#994 - 03/03/04 10:24 AM Re: compatibility of CHARMM [Re: firer]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The behavior of READ COOR PDB from files with more than one segment (chain) has changed a little between CHARMM versions. Try:
READ COOR PDB NAME filename RESID

CHARMM is much more comfortable with its own coordinate file format, which I would recommend for general CHARMM use, and save the READ/WRITE COOR PDB for situations where it is absolutely necessary.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top

Moderator:  John Legato, lennart