**From:** flavio seixas (*oivalf_nix_at_yahoo.com*)

**Date:** Wed Aug 04 2010 - 21:20:26 CDT

**Next message:**Ajasja Ljubetič: "Constraints on the plane and on the atom positions (in the same simulation)"**Previous message:**Ale Gomez: "Re: RetinalTop"**Next in thread:**Jim Phillips: "Re: Problems with AutoPSF"**Reply:**Jim Phillips: "Re: Problems with AutoPSF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Ajasja Ljubetič: "Constraints on the plane and on the atom positions (in the same simulation)"**Previous message:**Ale Gomez: "Re: RetinalTop"**Next in thread:**Jim Phillips: "Re: Problems with AutoPSF"**Reply:**Jim Phillips: "Re: Problems with AutoPSF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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