X-PLOR peptide blocking groups

Chris Sheldahl chris at neptune.cmc.uab.edu
Mon Aug 19 17:08:42 EST 1996


Hello X-PLOR'ers:

I'm having trouble with the acetylated N-terminus (ACE group)  
and the amide C-terminus peptide blocking groups (CT2 group) in 
X-PLOR (using the topallh22x.pro and parallh22x.pro files) . I am 
trying to generate the PSF file for a PDB file consisting of several 
peptides each of which is blocked with these groups. This works fine 
when I haven't blocked the ends of the peptides (ie when I use the 
standard N-terminus NTER and the standard C-terminus CTER). 
(I am changing the relevant sections of the toph19.pep linker file.) 
However, when I try to build hydrogens for the *capped* peptides during
PSF generation I get the following error:
 
 X-PLOR>flags exclude vdw elec end
 X-PLOR>hbuild
 HBUILD>  selection=( hydrogen )
 HBUILD>  phistep=4
 HBUILD>
 HBUILD>end
 HBUILD: dihedral PHI STePs for spin =    4.0000
 HBUILD: cutoff during water acceptor search =    7.5000
 %HBUILD-ERR: some parameters unknown -> terminating
 Subroutine DIE called . Terminating


This happens whether or not I have already added hydrogens to 
the capping groups before I try to generate the PSF file. Has anyone
else had a similar problem with either the ACE or CT2 groups? Are there
known problems with these groups? Any information or suggestions on this 
problem would be apprectiated.

Thanks in advance,
Christopher Sheldahl



More information about the Molmodel mailing list