[Xplor-nih] using charmm22

[Charles at Schwieters.org]

-----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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.py
Type: text/x-java
Size: 806 bytes
Desc: script with dynamics added
Url : http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20060920/9b292b71/test.bin
-------------- next part --------------
-----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-----