VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Dec 05 2009 - 15:40:27 CST

Hi Francesco,
could you paste the first few lines of your cg water psf? I doubt that
the atoms are named cgw; maybe CGW...?
Peter

Francesco Pietra wrote:
> Perhaps relevant (I forgot to mention), with all-atom water (by
> leaving "Use non-standard solvent" unchecked) there is no error
> message and the water box is shaped correctly around the elongated
> protein+membrane.
> francesco
>
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Sat, Dec 5, 2009 at 7:51 PM
> Subject: Fwd: vmd-l: Failure with AutoPSF (PDB has x, y, z zero)
> To: vmd <vmd-l_at_ks.uiuc.edu>
>
>
> 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
>>>
>>>