From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Feb 26 2007 - 08:40:24 CST
Hi Nabajyoti,
is psfgen, you should always split your file up so you have one pdb file
for each chain. In this case, the errors you see occur because psfgen
tries to treat your heme as part of a protein chain, and can't find the
appropriate residues to bond it to the rest of the protein. You may also
want to avoid atom names that contain spaces in your heme; there's some
confusion over whether those atoms are named NA or N A.
Peter
Nabajyoti Goswami wrote:
> Dear NAMD users,
>> I am very new to NAMD. I need to protonate some residues by using
>> patch command in the psfgen script. I am using the command as follows.
>>
>> package require psfgen
>> topology mytopology.inp
>> pdbalias residue HIS HSE
>> pdbalias residue HEM HEME
>> pdbalias atom ILE CD1 CD
>> segment U {pdb 2IIS.pdb}
>> patch HSP U:26 U:62 U:64 U:71 U:98 U:100 U:115
>> patch ASPP U:17 U:28 U:35 U:36 U:94
>> patch GLUP U:4 U:9 U:13 U:39 U:60 U:61
>> patch GLUP U:75 U:82 U:89 U:103 U:107
>> coordpdb 2IIS.pdb U
>> guesscoord
>> writepdb 2iis.pdb
>> writepsf 2iis.psf
>>
>> The topology file I have used has all protonated and neutral patches
>> of residues. I have got the PDB and PSF files but with the following
>> errors:
>> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>> <mailto:vmd_at_ks.uiuc.edu>
>> .........................................................................................
>> ERROR: Missing atoms for bond C(0) N(1) in residue THR:119
>> ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
>> in residue THR:119
>> ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0) CA(0)
>> C(0) N(1)
>> in residue THR:119
>> Missing atoms for conformation definition
>> Missing atoms for conformation definition
>> Missing atoms for conformation definition
>> U:1
>> Info: segment complete.
>> applying patch HSP to 7 residues
>> U:26 U:62 U:64 U:71 U:98 U:100 U:115
>> applying patch ASPP to 5 residues
>> U:17 U:28 U:35 U:36 U:94
>> applying patch GLUP to 6 residues
>> U:4 U:9 U:13 U:39 U:60 U:61
>> applying patch GLUP to 5 residues
>> U:75 U:82 U:89 U:103 U:107
>> reading coordinates from pdb file 2IIS.pdb for segment U
>> Warning: failed to set coordinate for atom OXT THR:119 U
>> Warning: failed to set coordinate for atom N A HEM:120 U
>> Warning: failed to set coordinate for atom N B HEM:120 U
>> Warning: failed to set coordinate for atom N C HEM:120 U
>> Warning: failed to set coordinate for atom N D HEM:120 U
>> Info: guessing coordinates for 963 atoms (4 non-hydrogen)
>> Warning: poorly guessed coordinates for 40 atoms (4 non-hydrogen):
>> Warning: poorly guessed coordinate for atom HT1 THR:1 U
>> Warning: poorly guessed coordinate for atom HT2 THR:1 U
>> Warning: poorly guessed coordinate for atom HT3 THR:1 U
>> Warning: poorly guessed coordinate for atom HE2 GLU:4 U
>> Warning: poorly guessed coordinate for atom HD2 ASP:17 U
>> Warning: poorly guessed coordinate for atom HE2 GLU:75 U
>> Warning: poorly guessed coordinate for atom NA HEME:120 U
>> Warning: poorly guessed coordinate for atom NB HEME:120 U
>> Warning: poorly guessed coordinate for atom NC HEME:120 U
>> Warning: poorly guessed coordinate for atom ND HEME:120 U
>> Warning: poorly guessed coordinate for atom HA HEME:120 U
>> Warning: poorly guessed coordinate for atom HB HEME:120 U
>> Warning: poorly guessed coordinate for atom HC HEME:120 U
>> Warning: poorly guessed coordinate for atom HD HEME:120 U
>> Warning: poorly guessed coordinate for atom HMA1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMA2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMA3
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAA1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAA2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBA1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBA2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMB1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMB2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMB3
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAB HEME:120 U
>> Warning: poorly guessed coordinate for atom HBB1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBB2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMC1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMC2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMC3
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAC HEME:120 U
>> Warning: poorly guessed coordinate for atom HBC1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBC2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMD1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMD2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HMD3
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAD1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HAD2
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBD1
>> HEME:120 U
>> Warning: poorly guessed coordinate for atom HBD2
>> HEME:120 U
>> Info: writing pdb file 2iis.pdb
>> Info: Atoms with guessed coordinates will have occupancy of 0.0.
>> Info: pdb file complete.
>> Info: writing psf file 2iis.psf
>> total of 1963 atoms
>> total of 2015 bonds
>> total of 3596 angles
>> total of 5298 dihedrals
>> total of 395 impropers
>> total of 117 cross-terms
>> Info: psf file complete.
>>
>> Can anyone help me out in this regard? How can I get rid off these
>> errors and warnings?
>>
>> thanks.
>> Nabajyoti Goswami
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