VMD-L Mailing List

From: Chaya Stern (chaya.stern_at_choderalab.org)
Date: Fri Oct 31 2014 - 14:08:07 CDT

Hello,

'm trying to add the ACE patch to the N-terminal but it seems like psfgen
is not finding the HN atom.

Here are the residue in the pdb:
        ATOM 1 N ASP P 23 18.447 -22.433 28.702 1.00
0.00 PROT N
    7 ATOM 2 HN ASP P 23 18.888 -23.323 28.586 1.00
0.00 PROT H
    8 ATOM 3 CA ASP P 23 19.440 -21.467 29.166 1.00
0.00 PROT C
    9 ATOM 4 HA ASP P 23 19.773 -21.804 30.141 1.00
0.00 PROT H
   10 ATOM 5 CB ASP P 23 20.644 -21.408 28.204 1.00
0.00 PROT C
   11 ATOM 6 HB1 ASP P 23 21.374 -20.663 28.578 1.00
0.00 PROT H
   12 ATOM 7 HB2 ASP P 23 21.149 -22.393 28.149 1.00
0.00 PROT H
   13 ATOM 8 CG ASP P 23 20.299 -20.994 26.784 1.00
0.00 PROT C
   14 ATOM 9 OD1 ASP P 23 20.550 -19.822 26.432 1.00
0.00 PROT O
   15 ATOM 10 OD2 ASP P 23 19.753 -21.834 26.037 1.00
0.00 PROT O
   16 ATOM 11 C ASP P 23 18.828 -20.078 29.364 1.00
0.00 PROT C
   17 ATOM 12 O ASP P 23 18.139 -19.579 28.474 1.00
0.00 PROT O

When I try to generate the patch for this residue, these are the errors I
get:

psfgen) building segment PROT
 94 psfgen) reading residues from pdb file ../pdb_files/frag0_protien.pdb
 95 psfgen) extracted 310 residues from pdb file
 96 psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.
 97 psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of
segment.
 98 psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
 99 psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
100 psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue ARG:344
101 psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
102 in residue ARG:344
103 psfgen) ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0)
CA(0) C(0) N(1)
104 in residue ARG:344
105 psfgen) Warning: missing atoms for conformation ARG CA-C-N-CA; skipping.
106 psfgen) Warning: missing atoms for conformation ARG N-CA-C-O; skipping.
107 psfgen) Warning: missing atoms for conformation ARG N-CA-C-N; skipping.
108 segment complete.
109 psfgen) reading coordinates from pdb file
./pdb_files/frag0_protien.pdb for segment PROT
110 psfgen) Warning: failed to set coordinate for atom HN ASP:23 PROT
111 psfgen) Warning: failed to set coordinate for atom HE2
GLU:122 PROT
112 psfgen) Warning: failed to set coordinate for atom OT1
ARG:344 PROT
113 psfgen) Warning: failed to set coordinate for atom OT2
ARG:344 PROT
114 psfgen) applying patch DISU to 2 residues
115 psfgen) applying patch DISU to 2 residues
116 psfgen) applying patch GLUP to 1 residues
117 psfgen) applying patch PLCY to 2 residues
118 psfgen) applying patch ACE to 1 residues
119 psfgen) no atom HN in residue ASP:23 of segment PROT
120 psfgen) Warning: add improper failed in patch ACE
121 psfgen) no atom HN in residue ASP:23 of segment PROT
122 psfgen) Warning: add conformation failed in patch ACE
123 psfgen) applying patch CT3 to 1 residues

This is what the resulting pdb looks like:
       ATOM 1 CAY ASP P 23 17.036 -23.161 29.064 0.00
0.00 PROT
    3 ATOM 2 HY1 ASP P 23 17.325 -23.525 28.178 0.00
0.00 PROT
    4 ATOM 3 HY2 ASP P 23 16.153 -22.702 28.972 0.00
0.00 PROT
    5 ATOM 4 HY3 ASP P 23 16.968 -23.903 29.730 0.00
0.00 PROT
    *6 ATOM 5 CY ASP P 23 17.716 -22.500 29.381 0.00
0.00 PROT*
    7 ATOM 6 OY ASP P 23 17.428 -22.137 30.267 0.00
0.00 PROT
    8 ATOM 7 N ASP P 23 18.447 -22.433 28.702 1.00
0.00 PROT N
    9 ATOM 8 HT1 ASP P 23 18.888 -23.323 28.586 0.00
0.00 PROT
   10 ATOM 9 HT2 ASP P 23 18.073 -22.122 27.828 0.00
0.00 PROT
   *11 ATOM 10 HT3 ASP P 23 17.716 -22.500 29.381 0.00
0.00 PROT*
   12 ATOM 11 CA ASP P 23 19.440 -21.467 29.166 1.00
0.00 PROT C
   13 ATOM 12 HA ASP P 23 19.773 -21.804 30.141 1.00
0.00 PROT H
   14 ATOM 13 CB ASP P 23 20.644 -21.408 28.204 1.00
0.00 PROT C

It places a CY and HT3 in the same spot. There's an HN in the topology file
for residue ASP so I don't know why psfgen is not finding it. It seems like
both the default and ACE termini are added here.

Thank you!