From: Maxwell Wesley Terban (mwt2115_at_columbia.edu)
Date: Fri Feb 28 2014 - 13:10:56 CST
I am trying to generate a .psf for a box of lactose molecules generated
from packmol.
I have a .pdb file from packmol (which I manually edited so the atom names
matched the topology file), and am using the top_all36_carb.rtf CHARMM
topology file to try and use the glucose and lactose molecules patched
together.
with the following .pgn file:
package require psfgen
resetpsf
topology ../forcefields/toppar_carb_apr12/top_all36_carb.rtf
segment LAC {
pdb alpha_smallBox.pdb
}
patch 14bb BGAL:1 AGLC:1
coordpdb alpha_smallBox.pdb LAC
guesscoord
writepdb alphaLactose_vmd.pdb
writepsf alphaLactose_vmd.psf
I get the output:
psfgen) Created by CHARMM version 32 1
psfgen) building segment LAC
psfgen) reading residues from pdb file alpha_smallBox.pdb
psfgen) extracted 100 residues from pdb file
psfgen) Info: generating structure...segment complete.
psfgen) applying patch 14BB to 2 residues
psfgen) no segment AGLC
ERROR: failed to apply patch
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
MOLECULE MISSING! Use resetpsf to start over.
My .pdb looks like this:
HEADER
TITLE Built with Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
HETATM 1 O4 BGALA 1 13.902 5.568 3.460 1.00
0.00 O
HETATM 2 O5 AGLCA 1 14.842 3.838 2.208 1.00
0.00 O
HETATM 3 O5 BGALA 1 15.646 6.078 6.669 1.00
0.00 O
HETATM 4 O3 BGALA 1 16.644 5.888 2.666 1.00
0.00 O
HETATM 5 O2 AGLCA 1 11.313 4.695 2.683 1.00
0.00 O
HETATM 6 O3 AGLCA 1 11.292 3.295 0.152 1.00
0.00 O
HETATM 7 O4 AGLCA 1 13.985 3.521 -0.498 1.00
0.00 O
HETATM 8 O2 BGALA 1 18.090 7.668 4.432 1.00
0.00 O
HETATM 9 O1 BGALA 1 16.102 8.372 6.283 1.00
0.00 O
HETATM 10 O6 BGALA 1 13.195 5.420 7.677 1.00
0.00 O
HETATM 11 O6 AGLCA 1 16.990 2.132 2.063 1.00
0.00 O
HETATM 12 C4 BGALA 1 14.996 5.540 4.374 1.00
0.00 C
HETATM 13 C3 BGALA 1 16.082 6.476 3.842 1.00
0.00 C
HETATM 14 C1 AGLCA 1 13.669 4.281 2.890 1.00
0.00 C
HETATM 15 C5 BGALA 1 14.533 5.968 5.774 1.00
0.00 C
HETATM 16 C2 AGLCA 1 12.487 4.401 1.927 1.00
0.00 C
HETATM 17 C3 AGLCA 1 12.278 3.095 1.161 1.00
0.00 C
HETATM 18 C4 AGLCA 1 13.584 2.613 0.530 1.00
0.00 C
HETATM 19 C2 BGALA 1 17.185 6.665 4.882 1.00
0.00 C
HETATM 20 C5 AGLCA 1 14.684 2.551 1.597 1.00
0.00 C
HETATM 21 C1 BGALA 1 16.615 7.042 6.250 1.00
0.00 C
HETATM 22 C6 BGALA 1 13.564 4.960 6.389 1.00
0.00 C
HETATM 23 C6 AGLCA 1 16.036 2.154 1.015 1.00
0.00 C
HETATM 24 H4 BGALA 1 15.431 4.532 4.456 1.00
0.00 H
HETATM 25 H3 BGALA 1 15.662 7.441 3.532 1.00
0.00 H
HETATM 26 H1 AGLCA 1 13.425 3.583 3.702 1.00
0.00 H
HETATM 27 H5 BGALA 1 14.020 6.937 5.731 1.00
0.00 H
HETATM 28 H2 AGLCA 1 12.629 5.237 1.229 1.00
0.00 H
HETATM 29 H3 AGLCA 1 11.890 2.325 1.839 1.00
0.00 H
HETATM 30 H4 AGLCA 1 13.438 1.638 0.053 1.00
0.00 H
HETATM 31 H5 AGLCA 1 14.416 1.835 2.386 1.00
0.00 H
HETATM 32 H2 BGALA 1 17.749 5.727 4.964 1.00
0.00 H
HETATM 33 H1 BGALA 1 17.423 7.020 6.988 1.00
0.00 H
HETATM 34 H61 BGALA 1 12.656 4.855 5.789 1.00
0.00 H
HETATM 35 H62 BGALA 1 14.030 3.975 6.505 1.00
0.00 H
HETATM 36 H61 AGLCA 1 15.995 1.161 0.558 1.00
0.00 H
HETATM 37 H62 AGLCA 1 16.388 2.872 0.269 1.00
0.00 H
HETATM 38 HO3 BGALA 1 15.925 5.790 2.018 1.00
0.00 H
HETATM 39 HO2 AGLCA 1 11.487 5.511 3.184 1.00
0.00 H
HETATM 40 HO3 AGLCA 1 10.486 3.618 0.592 1.00
0.00 H
HETATM 41 HO4 AGLCA 1 14.267 4.352 -0.079 1.00
0.00 H
HETATM 42 HO2 BGALA 1 18.779 7.766 5.112 1.00
0.00 H
HETATM 43 HO1 BGALA 1 15.746 8.590 5.406 1.00
0.00 H
HETATM 44 HO6 BGALA 1 14.008 5.511 8.202 1.00
0.00 H
HETATM 45 HO6 AGLCA 1 17.005 3.018 2.463 1.00
0.00 H
where this structure repeats for 99 more molecules, where the 1 goes to 100.
I cannot figure out what I am doing wrong, and cannot find any previous
questions about setting up homogeneous systems with many duplicates of the
same molecule.
Any suggestions or points toward the right direction would be greatly
appreciated. Thank you!
Max
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