PSFGEN

From: Hyun Chul Lee (lee252_at_purdue.edu)
Date: Mon Dec 07 2009 - 15:36:44 CST

I sent a question last week, but it wasn't posted.
I'm just a beginner in MD simulation. So I would appreciate if someone help me to solve my problem.

-------------------------------------------------
Here is my question

I'm working on generating ensemble structures of gold cluster labled proteins,
so added new residue which is called UDG in topology file and parameter files.

But when I run initial NAMD test I got ""FATAL ERROR: Multiplicity of Paramters for diehedral bond ..." errors.
As far as I figure out, this error came from generating PSF file using PSFGEN program with user defined residue (UDG).
I deleted all atoms except one in UDG, and run NAMD test. But I still got same results.

--------------------
The followings are simple examples (three amino acids plus dummy atom) which cause the same problem that I got in the gold cluster
labeled proteins.

-----------------------------------------------
#"test.pdb"
ATOM 1 N MET 1 53.882 -29.488 26.600 1.00 89.87 N
ATOM 2 CA MET 1 53.358 -28.278 25.877 1.00 90.31 C
ATOM 3 C MET 1 52.040 -28.493 25.123 1.00 91.07 C
ATOM 4 O MET 1 51.729 -29.610 24.666 1.00 93.30 O
ATOM 5 CB MET 1 54.436 -27.705 24.979 1.00 89.16 C
ATOM 6 CG MET 1 55.603 -27.244 25.797 1.00 89.35 C
ATOM 7 SD MET 1 56.229 -25.716 25.169 1.00 95.74 S
ATOM 8 CE MET 1 54.709 -24.639 25.257 1.00 94.48 C
ATOM 9 N GLU 2 51.298 -27.410 24.920 1.00 88.09 N
ATOM 10 CA GLU 2 49.982 -27.550 24.320 1.00 86.65 C
ATOM 11 C GLU 2 49.471 -26.556 23.297 1.00 83.87 C
ATOM 12 O GLU 2 50.143 -25.595 22.920 1.00 84.96 O
ATOM 13 CB GLU 2 48.972 -27.547 25.448 1.00 88.26 C
ATOM 14 CG GLU 2 49.000 -28.761 26.276 1.00 92.09 C
ATOM 15 CD GLU 2 47.624 -29.239 26.490 1.00 94.28 C
ATOM 16 OE1 GLU 2 47.137 -29.961 25.589 1.00 93.09 O
ATOM 17 OE2 GLU 2 47.038 -28.848 27.527 1.00 97.38 O1-
ATOM 18 N GLY 3 48.185 -26.729 22.984 1.00 78.60 N
ATOM 19 CA GLY 3 47.486 -25.845 22.085 1.00 68.74 C
ATOM 20 C GLY 3 47.227 -24.542 22.809 1.00 64.86 C
ATOM 21 O GLY 3 46.260 -23.852 22.518 1.00 62.22 O
ATOM 22 DUM UDG 4 47.932 -23.012 24.554 1.00 59.24 DUM

-----------------------------------------------
#newly added lines in "top_all22_prot_add.inp"
!For test [Here_to_edit]
RESI UDG 0.00
GROUP
ATOM DUM DUM 0.00

PRES UDGL 0.00 ! patch for GLY-DUM [Here_to_edit]
ATOM C C 0.00
ATOM DUM DUM 0.00
BOND C DUM

---------------------------------------
#test.tcl
# Create working directory; remove old output files
mkdir -p output
rm -f output/*

#(2) Embed the psfgen commands in this script
psfgen << ENDMOL

#(3) Read topology file
topology top_all22_prot_add.inp

#(4) Build protein segment
segment UDGP {
  pdb test.pdb
}

#(5) Patch protein to UDG
patch UDGL UDGP:3 UDGP:4

#(6) Read protein coordinates from PDB files
coordpdb test.pdb UDGP

#(9) Guess missing coordinates
guesscoord

#(10) Write structure and coordinate files
writepsf output/test_namd.psf
writepdb output/test_namd.pdb

----------------------------------------------
$ ./test.tcl

PSFGEN from NAMD 2.7b1 for MacOSX-x86
reading topology file top_all22_prot_add.inp

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum

Created by CHARMM version 31 1
cross-term entries present in topology definitions
building segment UDGP
reading residues from pdb file test.pdb
extracted 4 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
ERROR: Missing atoms for bond C(0) N(1) in residue GLY:3
ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
        in residue GLY:3
ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0) CA(0) C(0) N(1)
        in residue GLY:3
Missing atoms for conformation definition
Missing atoms for conformation definition
Missing atoms for conformation definition
UDGP:1
Info: segment complete.
applying patch UDGL to 2 residues
UDGP:3 UDGP:4
reading coordinates from pdb file test.pdb for segment UDGP
Info: guessing coordinates for 21 atoms (0 non-hydrogen)
Warning: poorly guessed coordinates for 4 atoms (0 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:1 UDGP
Warning: poorly guessed coordinate for atom HT2 MET:1 UDGP
Warning: poorly guessed coordinate for atom HT3 MET:1 UDGP
Warning: poorly guessed coordinate for atom DUM GLY:3 UDGP
Info: writing psf file output/test_namd.psf
total of 43 atoms
total of 41 bonds
total of 71 angles
total of 92 dihedrals
total of 5 impropers
total of 1 cross-terms
Info: psf file complete.
Info: writing pdb file output/test_namd.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
------------------------------------------------------------------

There could be a mistake in patching residue.
But I don't think this is the reason causing this error.

If anyone who knows how to debug this error, please let me know.

Thanks,
Hyun Chul Lee,

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