Thanks Charles, 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----- > > > >
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