From: tsaih_at_ncifcrf.gov
Date: Wed Mar 24 2004 - 14:35:43 CST
I am trying to setup system to calculate the aggregation of DFNKF peptides
(Asp1-Phe2-Asn3-Lys4-Phe5).
When I tried to generate PSF file by psfgen, it gave me these warning messages:
================================
Created by CHARMM version 27 1
building segment FR01
reading residues from pdb file fr01.pdb
extracted 5 residues from pdb file
generating structure at end of segment
no residue 1 before ASP:1 of segment FR01
Warning: add improper failed in residue ASP:1
no residue 1 before ASP:1 of segment FR01
Warning: add conformation C-N-CA-C failed in residue ASP:1
no residue 1 before ASP:1 of segment FR01
Warning: add conformation C-CA-N-HN failed in residue ASP:1
no residue 1 past PHE:5 of segment FR01
Warning: add bond C(0) N(1) failed in residue PHE:5
no residue 1 past PHE:5 of segment FR01
Warning: add improper failed in residue PHE:5
no residue 1 past PHE:5 of segment FR01
Warning: add conformation CA-C-N-CA failed in residue PHE:5
no residue 1 past PHE:5 of segment FR01
Warning: add conformation N-CA-C-O failed in residue PHE:5
no residue 1 past PHE:5 of segment FR01
Warning: add conformation N-CA-C-N failed in residue PHE:5
reading coordinates from pdb file fr01.pdb for segment FR01
writing psf file dfnkf.psf
total of 91 atoms
total of 92 bonds
total of 162 angles
total of 236 dihedrals
total of 14 impropers
writing pdb file dfnkf.pdb
============================
The warning messages are all for N and C-terminus. I checked the total numbers
of bonds, angles, dihedrals, and impropers, they are consistent with the
output from CHARMM. When I ignored these warning messages and submitted for
the MD simulations. The resulting structure contains abnormal bond lengths at
PHE:5.
Does any one have experience on these problems? any suggestion or advice is
appreciated! Thanks.
Gavin
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