VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 20:18:14 CDT

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