PSFGEN Warnings about H positions on standard amino acids

From: Bo Zhang (bozhang84_at_googlemail.com)
Date: Mon Feb 18 2008 - 07:07:39 CST

Hi,

I am trying to generate PSF using auto psf generator in VMD. I get the
following warnings about Hs added to standard amino acid residues. The
topology file is Charmm27. The LEU and PRO residue sections seem
fine. I tried using the topology file supplied with VMD and I get the
same msgs. I am assuming that minimization in NAMD with sort out any
 poorly positioned hydrogens, but I just wondered what could be
causing this?

Thanks in advance

Bo Zhang

Info: guessing coordinates for 3612 atoms (0 non-hydrogen)
Warning: poorly guessed coordinates for 49 atoms (0 non-hydrogen):
Warning: poorly guessed coordinate for atom HN1 PRO:1027 P1
Warning: poorly guessed coordinate for atom HN2 PRO:1027 P1
Warning: poorly guessed coordinate for atom HG LEU:1037 P1
Warning: poorly guessed coordinate for atom HG LEU:1058 P1
Warning: poorly guessed coordinate for atom HG LEU:1059 P1
Warning: poorly guessed coordinate for atom HG LEU:1067 P1
Warning: poorly guessed coordinate for atom HG LEU:1079 P1
Warning: poorly guessed coordinate for atom HG LEU:1098 P1
Warning: poorly guessed coordinate for atom HG LEU:1100 P1
Warning: poorly guessed coordinate for atom HG LEU:1121 P1
Warning: poorly guessed coordinate for atom HG LEU:1131 P1
Warning: poorly guessed coordinate for atom HG LEU:1138 P1
Warning: poorly guessed coordinate for atom HG LEU:1139 P1
Warning: poorly guessed coordinate for atom HG2 PRO:1147 P1
Warning: poorly guessed coordinate for atom HG LEU:1151 P1
Warning: poorly guessed coordinate for atom HG LEU:1154 P1
Warning: poorly guessed coordinate for atom HG2 PRO:1166 P1
Warning: poorly guessed coordinate for atom HG2 PRO:1173 P1
Warning: poorly guessed coordinate for atom HG LEU:1188 P1
Warning: poorly guessed coordinate for atom HG LEU:1214 P1
Warning: poorly guessed coordinate for atom HG LEU:1215 P1
Warning: poorly guessed coordinate for atom HG LEU:1227 P1
Warning: poorly guessed coordinate for atom HG LEU:1241 P1
Warning: poorly guessed coordinate for atom HG LEU:1249 P1
Warning: poorly guessed coordinate for atom HG LEU:1281 P1
Warning: poorly guessed coordinate for atom HG LEU:1283 P1
Warning: poorly guessed coordinate for atom HG LEU:1284 P1
Warning: poorly guessed coordinate for atom HG LEU:1295 P1
Warning: poorly guessed coordinate for atom HG LEU:1311 P1
Warning: poorly guessed coordinate for atom HG LEU:1316 P1
Warning: poorly guessed coordinate for atom HG LEU:1333 P1
Warning: poorly guessed coordinate for atom HE2 GLU:1338 P1
Warning: poorly guessed coordinate for atom HG LEU:1343 P1
Warning: poorly guessed coordinate for atom HG LEU:1354 P1
Warning: poorly guessed coordinate for atom HG LEU:1360 P1
Warning: poorly guessed coordinate for atom HT1 ALA:2003 P2
Warning: poorly guessed coordinate for atom HT2 ALA:2003 P2
Warning: poorly guessed coordinate for atom HT3 ALA:2003 P2
Warning: poorly guessed coordinate for atom HG LEU:2008 P2
Warning: poorly guessed coordinate for atom HG2 PRO:2020 P2
Warning: poorly guessed coordinate for atom HG LEU:2035 P2
Warning: poorly guessed coordinate for atom HG LEU:2043 P2
Warning: poorly guessed coordinate for atom HG2 PRO:2047 P2
Warning: poorly guessed coordinate for atom HG2 PRO:2048 P2
Warning: poorly guessed coordinate for atom HG LEU:2052 P2
Warning: poorly guessed coordinate for atom HG2 PRO:2064 P2
Warning: poorly guessed coordinate for atom HG LEU:2071 P2
Warning: poorly guessed coordinate for atom HG LEU:2095 P2
Warning: poorly guessed coordinate for atom HG2 PRO:2096 P2
Info: writing psf file mmroot_autopsf_tmpfile.psf
total of 7364 atoms
total of 7466 bonds
total of 13480 angles
total of 19839 dihedrals
total of 1250 impropers
total of 0 cross-terms
Info: psf file complete.
Info: writing pdb file mmroot_autopsf_tmpfile.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Autopsf: Updating structures
Autopsf: Updating structures
Autopsf: Updating structures
Loading the structure for rotation...
Autopsf: Updating structures

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