VMD-L Mailing List

From: Nd S (navdeep79_at_gmail.com)
Date: Thu Sep 18 2008 - 22:05:07 CDT

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>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