VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Dec 05 2009 - 12:51:22 CST

Hi Peter:
I repeated the solvation procedure to check for input errors, setting,
as before:

--Use Mol Dimensions

Box Padding 15 throughout

--Use non standard solvent

--Sol box pdb: cgwat.pdb

--Sol box psf: cgwat.psf

--Sol box top: rbcg-2007.top

Sol box side l: 40

Sol box key sel: name cgw

This time the log:

generating solute plus one replica of water...
generating water residue lists...
single water residue type, creating residue list...
replicating 64 water segments, 4 by 4 by

Therefore, I must assume that in previous trials I did some errors.
However, the screen output ends with:

nfo) Analyzing structure ...
Info) Atoms: 41282
Info) Bonds: 3845
Info) Angles: 5028 Dihedrals: 6136 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 38704
Info) Waters: 37308
Info) Segments: 102
Info) Fragments: 37437 Protein: 0 Nucleic: 0
Info) Using plugin pdb for coordinates from file solvate.pdb
Info) Finished with coordinate file solvate.pdb.
Info) Opened coordinate file solvate.pdb for writing.
Info) Extra structure overlap safety check...
-error Found 2273 water atoms near the solute! Please report this bug to
-error vmd_at_ks.uiuc.edu

Again, the box is cubic and the protein+membrane is not well centered.

francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Dec 5, 2009 at 5:07 PM
Subject: Re: vmd-l: Failure with AutoPSF (PDB has x, y, z zero)
To: Peter Freddolino <petefred_at_ks.uiuc.edu>

Hi Peter:
Sorry for bothering the users with my mistakes. I had forgot to
replace  with rbcg-2007.top the topology that comes automatically when
AutoPSF is opened. Now it works.

Solvation with AddSolvationBox cgwat did npot proceed as expected. I
got .psf .pdb files that open correctly, but errors were signaled
during the execution. Saved to log:

Running solvate with arguments:
cg_combined.popc+mod21.edited_autopsf.psf
cg_combined.popc+mod21.edited_autopsf.pdb -o solvate -s WT -x 15 -y 15
-z 15 +x 15 +y 15 +z 15 -b 2.4 -spdb cgwat.pdb -spsf cgwat.psf -stop
rbcg-2007.top -ws 40 -ks {name cgw}
generating solute plus one replica of water...
generating water residue lists...
single water residue type, creating residue list...
replicating 64 water segments, 4 by 4 by 4
 error $errMsg $savedInfo $savedCode }"
   (procedure "solvate" line 8)
   invoked from within
"solvate {cg_combined.popc+mod21.edited_autopsf.psf}
{cg_combined.popc+mod21.edited_autopsf.pdb} -o solvate -s WT -x 15 -y
15 -z 15 +x 15 +y 15 +z 15 -..."
   ("eval" body line 1)
   invoked from within
"eval solvate $command_line"
   (procedure "::Solvate::run_solvate" line 96)
   invoked from within
"::Solvate::run_solvate"
   invoked from within
".solvategui.solvate invoke"
   ("uplevel" body line 1)
   invoked from within
"uplevel #0 [list $w invoke]"
   (procedure "tk::ButtonUp" line 22)
   invoked from within
"tk::ButtonUp .solvategui.solvate"
   (command bound to event)

The box is cubic and too big for a Box Padding of 15 A. Also, the
protein+membrane is not centered in the water box. When I solvated the
protein alone with same settings

--Use mol dimensions
-- Box Padding 15
--topol rbcg-2007.top
--Side length 40
--key sel "name cgw"

the box was well shaped around the elongated protein. The protein +
membrane is elongated the same fashion.

Incidentally, does Autosolvationbox take into account clashes?

thanks

francesco

thanks
francesco

On Sat, Dec 5, 2009 at 3:21 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Francesco,
> did you use a CG topology file? It looks like you tried to use an all
> atom topology file with your CG protein, which is not going to work...
> Best,
> Peter
>
> Francesco Pietra wrote:
>> Hi:
>> I wonder whether by simply showing sections of an input
>> cg-protein-bilayer.pdb may suggest why the resulting pdb has zero
>> value for all coordinates, while the psf was formed. I used VMD 1.8.7
>> with the Nov 5, 2009 version of autopsf.tcl (sourced before using
>> AutoPSF, and used successfully with the cg-protein.pdb alone).
>>
>> Start of file:
>>
>> ATOM      1  BB  LEU A   1      94.117   6.647  33.003  1.00  0.00           C
>> ATOM      2 LEU2 LEU A   1      91.702   4.673  31.893  1.00  0.00           C
>> ATOM      3  BB  SER A   2      96.602   4.840  33.767  1.00  0.00           C
>>
>> ......................
>>
>>
>> End 1st subunit and start of 2nd (similarly for the other subunits):
>>
>> ATOM    834 LYS2 LYS A 426      87.486  15.560  52.901  1.00  0.00           C
>> ATOM    836  BB  LEU B   1      63.700  14.066  32.470  1.00  0.00           C
>> ATOM    837 LEU2 LEU B   1      62.820  11.464  34.800  1.00  0.00           C
>> ATOM    838  BB  SER B   2      66.653  14.844  33.474  1.00  0.00           C
>> ATOM    839 SER2 SER B   2      66.910  16.287  35.447  1.00  0.00           C
>>
>> .........................
>>
>> End of protein and start of lipid:
>>
>> ATOM   2484 ALA2 ALA C 419     100.557  15.272  22.450  1.00  0.00           C
>> ATOM   2485  BB  TYR C 420      99.103  10.800  24.846  1.00  0.00           C
>> ATOM   2486 TYR2 TYR C 420     101.793  14.152  26.627  1.00  0.00           C
>> ATOM      1 CHO  POPCL   1      45.698  63.146   8.734  1.00  0.00           N
>> ATOM      2 PHO  POPCL   1      48.402  64.504   6.458  1.00  0.00           P
>> ATOM      3 ES1  POPCL   1      49.993  59.387   4.107  1.00  0.00           C
>>
>> It may be noticed that the lipid atom name is placed at 13,14,15 while
>> in cg.membrane obtained with VMD is at 14,15,16. Actually, I combined
>> protein and membrane (and removed clashes) outside VMD (in the past I
>> was unable to do so with VMD).
>> ..................................
>>
>> "Interface" lipid-water:
>>
>> ATOM   2728 ME6  POPCL  19     109.251  34.896  60.703  1.00  0.00           C
>> ATOM   2729 MT2  POPCL  19     107.211  38.181  61.495  1.00  0.00           C
>> ATOM   2730 H2O  TIP3W   2     132.301  54.580  49.722  1.00  0.00           O
>> ATOM   2731 H2O  TIP3W  22     130.101  22.103  32.812  1.00  0.00           O
>> ATOM   2732 H2O  TIP3W  35     109.445  25.664  35.058  1.00  0.00           O
>>
>> .....................
>>
>> End of file:
>>
>> ATOM   3043 H2O  TIP3W4585     112.752  66.685  58.218  1.00  0.00           O
>> ATOM   3044 H2O  TIP3W4966     109.811  68.176  58.019  1.00  0.00           O
>> END
>> =================
>>
>> The output pdb:
>>
>> ATOM      1  N   LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   N
>> ATOM      2  HN  LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   H
>> ATOM      3  CA  LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   C
>>
>> The output psf:
>>
>> PSF CMAP
>>
>>      40 !NTITLE
>> REMARKS original generated structure x-plor psf file
>> REMARKS topology popc+mod21_autopsf-temp.top
>> REMARKS segment P1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment P2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment P3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O4 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O5 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O6 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O7 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O8 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O9 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O10 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O11 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O12 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O13 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O14 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O15 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O16 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O17 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O18 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O19 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O20 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O21 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O22 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O23 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O24 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O25 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O26 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O27 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O28 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O29 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O30 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O31 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W4 { first NONE; last NONE; auto angles dihedrals }
>>
>>   41610 !NATOM
>>       1 P1   1    LEU  N    NH1   -0.470000       14.0070           0
>>       2 P1   1    LEU  HN   H      0.310000        1.0080           0
>>       3 P1   1    LEU  CA   CT1    0.070000       12.0110           0
>>       4 P1   1    LEU  HA   HB     0.090000        1.0080           0
>>       5 P1   1    LEU  CB   CT2   -0.180000       12.0110           0
>>       6 P1   1    LEU  HB1  HA     0.090000        1.0080           0
>>       7 P1   1    LEU  HB2  HA     0.090000        1.0080           0
>>       8 P1   1    LEU  CG   CT1   -0.090000       12.0110           0
>>       9 P1   1    LEU  HG   HA     0.090000        1.0080           0
>> .........................
>> ..................
>> ===============
>>
>> Of course, this psf does not match with the input pdb.
>> =========
>>
>> thanks
>> francesco pietra
>>
>