Swanand
On 9/20/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello Swanand--
>
> I am trying to use charmm22 forcefield in xplor-nih. I believe the charmm22
> protein files are in toppar/charm22/***allh22x.pro. I copy those those files
> to toppar/charmm22.*** allh22x.pro and I run a simple script to read a
> protein, initialize its topology and parameters. I get this error :
>
> %PATCH-ERR: dihedral -C +N +CA +HA not found
> %PATCH-ERR: dihedral -C +N +CA +CB not found
> %PATCH-ERR: dihedral -CB -CA -C -OT2 not found
> %PATCH-ERR: dihedral -CB -CA -C -OT1 not found
> %PATCH-ERR: dihedral -HA -CA -C -OT2 not found
> %PATCH-ERR: dihedral -HA -CA -C -OT1 not found
These errors are due to atoms which don't exist. For instance, GLY has
no HA atom (at the C terminus). I think the resulting structure should
be fine, though.
>
> I have attached my script and output, and also the inputs sequence file and
> coordinates.
I modified your script to perform some dynamics, and all seems ok- it is
attached.
regards--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.5 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/>
iD8DBQFFEXHxPK2zrJwS/lYRAm+UAJ9hP4VqSM9AAhRbGg8tEL0Vp/qgvgCfXS23
GAfCjHrKhxbnVANGZCgV3lY=
=vZFy
-----END PGP SIGNATURE-----
--
You must be the change you wish to see in the world. (M K Gandhi)
_______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
