VMD-L Mailing List

From: David Alejandro Rincón Daza (darincond_at_unal.edu.co)
Date: Tue Jun 02 2020 - 16:51:19 CDT

Hi, I am trying to build a PSF file. The commands that I am using are:

in VMD -> Extension -> Tk console

*set MCC_ORI [atomselect top protein]*

* $MCC_ORI writepdb MCC_ORI_protein.pdb*

* set MCC_ORI [atomselect top "resname TOL"]*

* $MCC_ORI writepdb MCC_ORI_solvent.pdb*

* set MCC_ORI [atomselect top water]*

* $MCC_ORI writepdb MCC_ORI_water.pdb*

* set MCC_ORI [atomselect top "resname SUB"]*

* $MCC_ORI writepdb MCC_ORI_sub.pdb*

Then, I create a png file:

*package require psfgen*

* topology top_all27_prot_lipid_withSEA_TOL_TI_test2_02_link.rtf*

* segment PROT {pdb MCC_ORI_protein.pdb}*

*coordpdb MCC_ORI_protein.pdb PROT*

* segment PROP {pdb MCC_ORI_sub.pdb}*

* coordpdb MCC_ORI_sub.pdb PROP*

* segment XWAT {pdb MCC_ORI_water.pdb}*

*coordpdb MCC_ORI_water.pdb XWAT*

* segment SOLV {pdb MCC_ORI_solvent.pdb}*

* coordpdb MCC_ORI_solvent.pdb SOLV*

*guessscoord*

* writepdb MCC_ORI_mod.pdb*

* writepsf MCC_ORI_mod.psf *

and I get this info at the end of the process:

*psfgen) Info: guessing coordinates for 24 atoms (9 non-hydrogen)psfgen)
Warning: failed to guess coordinates for 17 atomspsfgen) Info: writing pdb
file MCC_ORI_mod_all36.pdbpsfgen) Info: Atoms with guessed coordinates will
have occupancy of 0.0.*

When I do awk to the new pdb file:

*awk '$9=="-1.00"' a*

*ATOM 301 HG1 CYS 22 0.000 0.000 0.000 -1.00 0.00
 PROT ATOM 898 HG1 CYS 64 0.000 0.000 0.000 -1.00 0.00
   PROT ATOM 3165 HG1 CYS 216 0.000 0.000 0.000 -1.00 0.00
     PROT ATOM 3286 HE2 HSP 224 0.000 0.000 0.000 -1.00
 0.00 PROT ATOM 3772 HG1 CYS 258 0.000 0.000 0.000
-1.00 0.00 PROT ATOM 4258 HG1 CYS 293 0.000 0.000
0.000 -1.00 0.00 PROT ATOM 4542 HG1 CYS 311 0.000 0.000
  0.000 -1.00 0.00 PROT ATOM 4627 N SUB 1 0.000
0.000 0.000 -1.00 0.00 PROP ATOM 4628 HT1 SUB 1 0.000
  0.000 0.000 -1.00 0.00 PROP ATOM 4629 HT2 SUB 1
0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4630 HT3 SUB 1
  0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4631 CA SUB 1
    0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4632 HA SUB 1
      0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4633 C SUB
 1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4634 OT1 SUB
   1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4635 OT2
SUB 1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 5528 N
  TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM 5529
 HT1 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM
5530 HT2 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM
  5531 HT3 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV
 ATOM 5544 HA TOL 1 0.000 0.000 0.000 -1.00 0.00
 SOLV ATOM 21808 C TOL 1086 0.000 0.000 0.000 -1.00 0.00
   SOLV ATOM 21809 OT1 TOL 1086 0.000 0.000 0.000 -1.00 0.00
     SOLV ATOM 21810 OT2 TOL 1086 0.000 0.000 0.000 -1.00
 0.00 SOLV *

I obtain 24 atoms with the same coordinates. Moreover, this new pdb file is
24 atoms larger than the original pdb.

Questions:

*How can I avoid that?*
*How can I remove them?*
*Is it useful to rename those atoms as DUM?*

Looking forward
Thanks in advance