VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Mar 11 2010 - 17:48:11 CST

You claim you aligned the PCGL with the PALM residues, but that doesn't seem to be the case at all. The PCGL is somewhere in the middle of the two tails, and inverted.

On Mar 11, 2010, at 5:06 PM, Ronald Salesky wrote:

> Hi JC,
>
> Thank you. Unfortunately, the "rubber-band" bonds still are there after using coordpdb properly. I've attached the resulting dppc.pdb and dppc.psf so you can see what I mean. Is this due to improper placement of the 2 PALMs before doing the patch, or...? Thank you for your help and suggestions.
>
> Best,
>
> Ron
>
> On Wed, 10 Mar 2010 22:56:48 -0600
> "JC Gumbart" <gumbart_at_ks.uiuc.edu> wrote:
>> 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 %
>
> <dppc.pdb><dppc.psf>