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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-----
