VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Mar 10 2010 - 22:56:48 CST

The proper use of coordpdb includes the segname at the end. So you should
be using, e.g., "coordpdb palm1.pdb plm1".

However, I've always hated this modular form for DPPC. You might be happier
with these files provided by Jeff Klauda:
http://terpconnect.umd.edu/~jbklauda/research/download.html

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Ronald Salesky
Sent: Wednesday, March 10, 2010 6:34 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: properly applying patches to create DPPC

Hi,

I have been attempting to create a DPPC lipid from two PALM residues and a
PCGL residue with the EST1 and EST2 patches as described in the topology
file and in the VMD mailing list archives. The result is always a molecule
with long "rubber-bandy" looking bonds once the patches are applied. The
coordinates for each of the respective residues were obtained from the
CHARMM small molecule library. Each residue is loaded from its own
respective .pdb file and each PALM has its own segment name. I loaded the 3
residues in the VMD viewer and moved each palm so that its C1 atom was near
O1 and O2 of PCGL respectively and saved the coordinates thinking this was
the problem, but no improvement was obtained. Any suggestions on obtaining a
proper looking DPPC molecule would be most appreciated!

The Tk console commands are below and I've attached the respective .pdb
files for reference.

Cheers,

Ron Salesky
Research assistant, Nanoscience and Microsystems University of New Mexico

-------------------------------------------------------
First just the tcl commands used w/o command results:

topology
../plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
package require psfgen
segment plm1 {
pdb palm1.pdb
first none
last none }
segment plm2 {
pdb palm2.pdb
first none
last none }
segment pcgl {
pdb pcgl.pdb
first none
last none }
coordpdb palm1.pdb
coordpdb palm2.pdb
coordpdb pcgl.pdb
guesscoord
patch EST1 pcgl:1 plm1:1
patch EST2 pcgl:1 plm2:1
regenerate angles dihedrals
writepdb dppc.pdb
writepsf dppc.psf

-------------------------------------------------------------------------
The raw Tkconsole output w/ command results:

Main console display active (Tcl8.5.6 / Tk8.5.6)
(vmd-1.8.7) 1 % cd DPPC
>Main< (DPPC) 2 % topology
>../plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
reading topology file
../plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp

>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
from
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
and
   \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
   \\\\\\\\\\\\\\\\\\ Developmental
/////////////////////////
               Alexander D. MacKerell Jr.
                      August 1999
  All comments to ADM jr. email: alex,mmiris.ab.umd.edu
               telephone: 410-706-7442

Created by CHARMM version 27 1
cross-term entries present in topology definitions
>Main< (DPPC) 3 % package require psfgen
1.4.7
>Main< (DPPC) 4 % segment plm1 {
pdb palm1.pdb
first none
last none }
building segment PLM1
reading residues from pdb file palm1.pdb extracted 1 residues from pdb file
setting patch for first residue to NONE setting patch for last residue to
NONE
Info: generating structure...
Info: segment complete.
>Main< (DPPC) 5 % segment plm2 {
pdb palm2.pdb
first none
last none }
building segment PLM2
reading residues from pdb file palm2.pdb extracted 1 residues from pdb file
setting patch for first residue to NONE setting patch for last residue to
NONE
Info: generating structure...
Info: segment complete.
>Main< (DPPC) 6 % segment pcgl {
pdb pcgl.pdb
first none
last none }
building segment PCGL
reading residues from pdb file pcgl.pdb
extracted 1 residues from pdb file
setting patch for first residue to NONE
setting patch for last residue to NONE
Info: generating structure...
Info: segment complete.
>Main< (DPPC) 7 % coordpdb palm1.pdb
reading coordinates from pdb file palm1.pdb
>Main< (DPPC) 8 % coordpdb palm2.pdb
reading coordinates from pdb file palm2.pdb
>Main< (DPPC) 9 % coordpdb pcgl.pdb
reading coordinates from pdb file pcgl.pdb
Warning: failed to set coordinate for atom H11 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H12 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H21 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H22 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H23 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H31 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H32 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H33 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H41 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H42 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H43 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H51 PCGL:1
 PCGL
Warning: failed to set coordinate for atom H52 PCGL:1
 PCGL
Warning: failed to set coordinate for atom O3 PCGL:1
 PCGL
Warning: failed to set coordinate for atom O4 PCGL:1
 PCGL
Warning: failed to set coordinate for atom CG1 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HG11 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HG12 PCGL:1
 PCGL
Warning: failed to set coordinate for atom CG2 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HG21 PCGL:1
 PCGL
Warning: failed to set coordinate for atom OG2 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HO2 PCGL:1
 PCGL
Warning: failed to set coordinate for atom CG3 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HG31 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HG32 PCGL:1
 PCGL
Warning: failed to set coordinate for atom OG3 PCGL:1
 PCGL
Warning: failed to set coordinate for atom HO3 PCGL:1
 PCGL
>Main< (DPPC) 10 % guesscoord
Info: guessing coordinates for 27 atoms (7 non-hydrogen)
Warning: poorly guessed coordinates for 27 atoms (7
non-hydrogen):
Warning: poorly guessed coordinate for atom C6 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom C7 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom C8 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H5A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H5B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H6A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H6B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H6C PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H7A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H7B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H7C PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H8A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H8B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H8C PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H4A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H4B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom OP3 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom OP4 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom OP1 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom OP2 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H3A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H3B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H2A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H2 PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H1A PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H1B PCGL:1
 PCGL
Warning: poorly guessed coordinate for atom H1 PCGL:1
 PCGL
>Main< (DPPC) 11 % patch EST1 pcgl:1 plm1:1
applying patch EST1 to 2 residues
>Main< (DPPC) 12 % patch EST2 pcgl:1 plm2:1
applying patch EST2 to 2 residues
>Main< (DPPC) 13 % regenerate angles dihedrals
regenerating all angles
regenerating all dihedrals
>Main< (DPPC) 14 % writepdb dppc.pdb
Info: writing pdb file dppc.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
>Main< (DPPC) 15 % writepsf dppc.psf
Info: writing psf file dppc.psf
total of 130 atoms
total of 129 bonds
total of 250 angles
total of 348 dihedrals
total of 0 impropers
total of 0 cross-terms
Info: psf file complete.
>Main< (DPPC) 16 %