From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Mar 01 2014 - 21:41:45 CST
This line from your error is the clue:
psfgen) no segment AGLC
The way patches work is that you use:
patch patchname segname1:resid1 segname2:resid2
not residue name. The problem is that in your case, two residues are given the same number (the ordering of the atoms may also be a problem but maybe not?). Best would be to write a little script in VMD to renumber them sequentially (so you have 200 residues instead of 100) OR break up the PDBs into two, one with all the AGLC and one with all the BGAL residues, and then create two segments in psfgen and link them accordingly.
On Feb 28, 2014, at 2:10 PM, Maxwell Wesley Terban <mwt2115_at_columbia.edu> wrote:
> 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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