VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 22:14:25 CDT

Hi Navdeep,
I'm afraid I don't understand your question now...
once autopsf finished you should have files Alcohol_autopsf.psf and
Alcohol_autopsf.pdb, which will be the finished files. You should be
able to write topology entries for larger molecules following the same
principles as you did for ethanol (and since this was your aim I
certainly understand you wanting to make the file yourself).
Best,
Peter

Nd S wrote:
> Thanks Peter.
>
> Actually I am practicing making residue. Also I have added the above
> residue in the "top_all27_prot_lipid_na.inp" file. I just sent in the
> residue I have written.
>
> Output of Console
>
> info) Finished with coordinate file /home/Alcohol.pdb.
> Info) Opened coordinate file Alcohol_autopsf-temp.pdb for writing.
> Info) Opened coordinate file Alcohol_autopsf-temp.xbgf for writing.
> Info) Finished with coordinate file Alcohol_autopsf-temp.pdb.
> Info) Finished with coordinate file Alcohol_autopsf-temp.xbgf.
>
> Output of Alcohol_autopsf-temp.pdb
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 C1 ETALX 1 -0.833 -0.385 -0.123 1.00
> 0.00 C
> ATOM 2 C2 ETALX 1 0.550 0.243 -0.380 1.00
> 0.00 C
> ATOM 3 O1 ETALX 1 1.408 0.092 0.854 1.00
> 0.00 O
> ATOM 4 H11 ETALX 1 -0.708 -1.492 0.120 1.00
> 0.00 H
> ATOM 5 H12 ETALX 1 -1.481 -0.271 -1.054 1.00
> 0.00 H
> ATOM 6 H13 ETALX 1 -1.332 0.143 0.755 1.00
> 0.00 H
> ATOM 7 H21 ETALX 1 0.425 1.350 -0.623 1.00
> 0.00 H
> ATOM 8 H22 ETALX 1 1.050 -0.285 -1.258 1.00
> 0.00 H
> ATOM 9 HO1 ETALX 1 0.920 0.605 1.708 1.00
> 0.00 H
> END
>
> Output of Alcohol_autopsf-temp.xbgf.
>
> BIOGRF 332
> REMARK NATOM 9
> FORCEFIELD DREIDING
> FORMAT ATOM
> (a6,1x,i6,1x,a5,1x,a4,1x,a1,1x,i5,3f10.5,1x,a5,i3,i2,1x,f8.5,1x,f6.3,1x,f6.3,1x,i3,1x,a4)
> ATOM 1 C1 ETAL X 1 -0.83300 -0.38500 -0.12300 C1
> 0 0 0.00000 0.000 1.000 6
> ATOM 2 C2 ETAL X 1 0.55000 0.24300 -0.38000 C2
> 0 0 0.00000 0.000 1.000 6
> ATOM 3 O1 ETAL X 1 1.40800 0.09200 0.85400 O1
> 0 0 0.00000 0.000 1.000 8
> ATOM 4 H11 ETAL X 1 -0.70800 -1.49200 0.12000 H11
> 0 0 0.00000 0.000 1.000 1
> ATOM 5 H12 ETAL X 1 -1.48100 -0.27100 -1.05400 H12
> 0 0 0.00000 0.000 1.000 1
> ATOM 6 H13 ETAL X 1 -1.33200 0.14300 0.75500 H13
> 0 0 0.00000 0.000 1.000 1
> ATOM 7 H21 ETAL X 1 0.42500 1.35000 -0.62300 H21
> 0 0 0.00000 0.000 1.000 1
> ATOM 8 H22 ETAL X 1 1.05000 -0.28500 -1.25800 H22
> 0 0 0.00000 0.000 1.000 1
> ATOM 9 HO1 ETAL X 1 0.92000 0.60500 1.70800 HO1
> 0 0 0.00000 0.000 1.000 1
> FORMAT CONECT (a6,14i6)
> FORMAT ORDER (a6,i6,13f6.3)
> CONECT 1
> ORDER 1
> CONECT 2
> ORDER 2
> CONECT 3
> ORDER 3
> CONECT 4
> ORDER 4
> CONECT 5
> ORDER 5
> CONECT 6
> ORDER 6
> CONECT 7
> ORDER 7
> CONECT 8
> ORDER 8
> CONECT 9
> ORDER 9
> END
>
>
> Any help will enable me to write residues for complex molecules.
>
> Navdeep
>
> On Thu, Sep 18, 2008 at 8:18 PM, Peter Freddolino
> <petefred_at_ks.uiuc.edu <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Hi Navdeep,
> it's generally helpful to check the console for additional output.
> In this case, you didn't include any MASS lines (needed to
> enumerate the atom types that are present and define their
> masses), so psfgen doesn't recognize your atom types. See the top
> of one of the standard topology files for an example.
> BTW, any reason you didn't just use the ETOH residue from
> toppar_all22_prot_model.str? It's in the stream directory of the
> charmm forcefield distribution.
> Peter
>
>
> Nd S wrote:
>
> Hi all
>
> I am trying to generate psf files using auto psfgen, for ethyl
> alcohol, by defining the residue. I am getting the following
> error:
>
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "segment $segid {
> pdb $segfile
>
> # We alias the C-terminal OXT atoms to OT2 so that psfgen
> has to guess one atom less.
> # Otherwise psf..."
> (procedure "psfsegments" line 29)
> invoked from within
> "psfsegments $logfileout"
> (procedure "::autopsf::afterchains_gui" line 50)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish
> "
> (command bound to event)
>
> I have defined the residue as:
>
> Resi ETAL 0.00 !Ethyl Alcohol, Navdeep
> Group
> Atom C1 CTL3 -0.27 !
> Atom H11 HAL3 0.09 !
> Atom H12 HAL3 0.09 ! H11 O1--HO1
> Atom H13 HAL3 0.09 ! \ /
> Group ! H12--C1-C2--H21
> Atom C2 CTL2 0.05 ! / \
> Atom O1 OH1 -0.66 ! H13 H22
> Atom H21 HAL2 0.09 !
> Atom H22 HAL2 0.09 !
> Atom HO1 HO 0.43 !
> Bond C1 H11 C1 H12 C1 H13
> Bond C1 C2
> Bond C2 O1
> Bond C2 H21 C2 H22
> Bond O1 HO1
> IC O1 C2 C1 H11 0.00 0.00 -60.0 0.0 0.0
> IC H11 C1 C2 H22 0.00 0.00 60.0 0.0 0.0
> IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0
> IC O1 C2 C1 H12 0.00 0.00 180.0 0.0 0.0
> IC H13 C1 C2 H21 0.00 0.00 -60.0 0.0 0.0
> IC C1 C2 O1 HO1 0.00 0.00 -60.0 0.0 0.0
> IC HO1 O1 C2 H21 0.00 0.00 60.0 0.0 0.0
> patc firs none last none
>
> and the pdb file I am using is:
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1
> 1
> ATOM 1 C1 ETALX 1 -0.833 -0.385 -0.123 1.00
> 0.00 C
> ATOM 2 C2 ETALX 1 0.550 0.243 -0.380 1.00
> 0.00 C
> ATOM 3 O1 ETALX 1 1.408 0.092 0.854 1.00
> 0.00 O
> ATOM 4 H11 ETALX 1 -0.708 -1.492 0.120 1.00
> 0.00 H
> ATOM 5 H12 ETALX 1 -1.481 -0.271 -1.054 1.00
> 0.00 H
> ATOM 6 H13 ETALX 1 -1.332 0.143 0.755 1.00
> 0.00 H
> ATOM 7 H21 ETALX 1 0.425 1.350 -0.623 1.00
> 0.00 H
> ATOM 8 H22 ETALX 1 1.050 -0.285 -1.258 1.00
> 0.00 H
> ATOM 9 HO1 ETALX 1 0.920 0.605 1.708 1.00
> 0.00 H
> END
>
> Thanks
>
> Navdeep
>
>
>
>
> --
> --------------------------------------------
> Gig'em
> Navdeep Singh