Re: Problems with AutoPSF

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Aug 06 2010 - 09:36:28 CDT

Those "poorly guessed coordinates" warnings are not unusual. It just
means psfgen had to use an internal heuristic rather than the pdb file or
a rule in the topology file to assign positions to those atoms. If the
system looks normal, minimizes, and runs you're probably fine. If not,
those atoms are a good place to look.

-Jim

On Wed, 4 Aug 2010, flavio seixas wrote:

> Hi All,
>
> I am trying to generate a psf file of a hemoglobin molecule with 4 heme groups and 2 water molecules using AutoPSF plugin on VMD.
>
> I did not find any solution in namd-list archives.
>
> Someone could give me any suggestion?
>
> Using charm parameters and topology files I received this message (final part of the message):
>
>
> reading coordinates from pdb file HbS_pdbset1_autopsf-temp.pdb_W1.pdb for segment W1
> Determine S-S bonds based on distance <3.0A
> Info: guessing coordinates for 4516 atoms (4 non-hydrogen)
> Warning: poorly guessed coordinates for 140 atoms (4 non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1 VAL:1 P1
> Warning: poorly guessed coordinate for atom HT2 VAL:1 P1
> Warning: poorly guessed coordinate for atom HT3 VAL:1 P1
> Warning: poorly guessed coordinate for atom OT1 ARG:141 P1
> Warning: poorly guessed coordinate for atom HA HEME:142 O1
> Warning: poorly guessed coordinate for atom HB HEME:142 O1
> Warning: poorly guessed coordinate for atom HC HEME:142 O1
> Warning: poorly guessed coordinate for atom HD HEME:142 O1
> Warning: poorly guessed coordinate for atom HMA1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMA2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMA3 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAA1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAA2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBA1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBA2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMB1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMB2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMB3 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAB HEME:142 O1
> Warning: poorly guessed coordinate for atom HBB1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBB2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMC1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMC2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMC3 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAC HEME:142 O1
> Warning: poorly guessed coordinate for atom HBC1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBC2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMD1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMD2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HMD3 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAD1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HAD2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBD1 HEME:142 O1
> Warning: poorly guessed coordinate for atom HBD2 HEME:142 O1
> Warning: poorly guessed coordinate for atom HT1 VAL:1 P2
> Warning: poorly guessed coordinate for atom HT2 VAL:1 P2
> Warning: poorly guessed coordinate for atom HT3 VAL:1 P2
> Warning: poorly guessed coordinate for atom OT1 HSD:146 P2
> Warning: poorly guessed coordinate for atom HA HEME:147 O2
> Warning: poorly guessed coordinate for atom HB HEME:147 O2
> Warning: poorly guessed coordinate for atom HC HEME:147 O2
> Warning: poorly guessed coordinate for atom HD HEME:147 O2
> Warning: poorly guessed coordinate for atom HMA1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMA2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMA3 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAA1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAA2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBA1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBA2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMB1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMB2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMB3 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAB HEME:147 O2
> Warning: poorly guessed coordinate for atom HBB1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBB2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMC1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMC2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMC3 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAC HEME:147 O2
> Warning: poorly guessed coordinate for atom HBC1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBC2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMD1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMD2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HMD3 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAD1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HAD2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBD1 HEME:147 O2
> Warning: poorly guessed coordinate for atom HBD2 HEME:147 O2
> Warning: poorly guessed coordinate for atom HT1 VAL:1 P3
> Warning: poorly guessed coordinate for atom HT2 VAL:1 P3
> Warning: poorly guessed coordinate for atom HT3 VAL:1 P3
> Warning: poorly guessed coordinate for atom OT1 ARG:141 P3
> Warning: poorly guessed coordinate for atom HA HEME:142 O3
> Warning: poorly guessed coordinate for atom HB HEME:142 O3
> Warning: poorly guessed coordinate for atom HC HEME:142 O3
> Warning: poorly guessed coordinate for atom HD HEME:142 O3
> Warning: poorly guessed coordinate for atom HMA1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMA2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMA3 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAA1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAA2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBA1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBA2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMB1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMB2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMB3 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAB HEME:142 O3
> Warning: poorly guessed coordinate for atom HBB1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBB2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMC1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMC2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMC3 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAC HEME:142 O3
> Warning: poorly guessed coordinate for atom HBC1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBC2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMD1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMD2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HMD3 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAD1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HAD2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBD1 HEME:142 O3
> Warning: poorly guessed coordinate for atom HBD2 HEME:142 O3
> Warning: poorly guessed coordinate for atom HT1 VAL:1 P4
> Warning: poorly guessed coordinate for atom HT2 VAL:1 P4
> Warning: poorly guessed coordinate for atom HT3 VAL:1 P4
> Warning: poorly guessed coordinate for atom OT1 HSD:146 P4
> Warning: poorly guessed coordinate for atom HA HEME:147 O4
> Warning: poorly guessed coordinate for atom HB HEME:147 O4
> Warning: poorly guessed coordinate for atom HC HEME:147 O4
> Warning: poorly guessed coordinate for atom HD HEME:147 O4
> Warning: poorly guessed coordinate for atom HMA1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMA2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMA3 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAA1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAA2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBA1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBA2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMB1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMB2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMB3 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAB HEME:147 O4
> Warning: poorly guessed coordinate for atom HBB1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBB2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMC1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMC2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMC3 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAC HEME:147 O4
> Warning: poorly guessed coordinate for atom HBC1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBC2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMD1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMD2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HMD3 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAD1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HAD2 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBD1 HEME:147 O4
> Warning: poorly guessed coordinate for atom HBD2 HEME:147 O4
> Warning: poorly guessed coordinate for atom H1 TIP3:1 W1
> Warning: poorly guessed coordinate for atom H2 TIP3:1 W1
> Warning: poorly guessed coordinate for atom H1 TIP3:2 W1
> Warning: poorly guessed coordinate for atom H2 TIP3:2 W1
>
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