From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Dec 17 2010 - 10:58:39 CST
The reason for the zeros is that you have atoms with the same name in the
same residue. Unlike the normal VMD molecule file readers, the psfgen
coordpdb command does not assume that the atomids in the pdb file match
those of the internal structure. It uses segname, resid, and atom name to
assign coordinates to atoms. In your case it is assigning both sets of
C_1 and C_2 coordinates to the first C_1 and C_2 atoms in the residue.
ATOM 1 C_1 C_G X 99 -20.353 -38.745 -3.350 1.00 0.00 C_G
ATOM 2 C_2 C_G X 99 -21.063 -37.515 -3.350 1.00 0.00 C_G
ATOM 3 C_1 C_G X 99 0.000 0.000 0.000 -1.00 0.00 C_G
ATOM 4 C_1 C_G X 100 -16.093 -38.745 -3.350 1.00 0.00 C_G
ATOM 5 C_2 C_G X 100 -18.933 -38.745 -3.350 1.00 0.00 C_G
ATOM 6 C_2 C_G X 100 0.000 0.000 0.000 -1.00 0.00 C_G
ATOM 7 C_1 C_G X 100 0.000 0.000 0.000 -1.00 0.00 C_G
ATOM 8 C_1 C_G X 101 -11.833 -38.745 -3.350 1.00 0.00 C_G
ATOM 9 C_2 C_G X 101 -14.673 -38.745 -3.350 1.00 0.00 C_G
ATOM 10 C_2 C_G X 101 0.000 0.000 0.000 -1.00 0.00 C_G
ATOM 11 C_1 C_G X 101 0.000 0.000 0.000 -1.00 0.00 C_G
Give every atom in a residue a unique name and it should work.
-Jim
On Fri, 17 Dec 2010, 何毓辉 wrote:
> Sorry for the mistake.
>
> Thanks!
>
> 2010/12/17 Jim Phillips <jim_at_ks.uiuc.edu>
>
>>
>> Your script complains:
>>
>> couldn't open "SiN_pore.bound": no such file or directory
>>
>> Can you just send the graphene psf file too?
>>
>>
>> -Jim
>>
>>
>> On Wed, 15 Dec 2010, 何毓辉 wrote:
>>
>> Dear Jim,
>>>
>>> Thanks very much for your attention!
>>>
>>> Attached are the tcl files and input graphene PDB file. The script
>>> 1_generateGraphenePsf.tcl constructs the PSF file of graphene, by
>>> measuring
>>> atom distances and then determining the bonds and angles. The script
>>> 2_combineNanopore.tcl merges SiN and graphene, where error happens.
>>> In fact, I tried keeping only the graphene part by deleting the
>>> commands "readpsf $psf1; coordpdb $pdb1", but it still resulted in error
>>> position.
>>>
>>> Please have a look.
>>> Thanks again!
>>>
>>> He Yuhui
>>>
>>> On Dec 15, 2010 2:32pm, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>>
>>>>
>>>>
>>>> Can you send the input files so I can diagnose this? -Jim
>>>>
>>>>
>>>>
>>>> On Wed, 15 Dec 2010, 何毓辉 wrote:
>>>>
>>>>
>>>>
>>>>
>>>> Dear All,
>>>>
>>>>
>>>>
>>>> I construct the pdb and psf files of a single-layer graphene, by
>>>>
>>>> following the approach shown in the tutorial "Modeling Nanopores for
>>>>
>>>> Sequencing DNA".
>>>>
>>>>
>>>>
>>>> (Maybe it is helpful to give more details for the construction: first,
>>>>
>>>> the pdb file of a single-layer graphene is constructed by recording
>>>>
>>>> positions of each carbon atom on the graphene; then, sigma-bonds are
>>>>
>>>> determined and recorded by measuring the distance between each two carbon
>>>>
>>>> atoms; after that, angles formed by two neighbouring sigma-bonds are
>>>>
>>>> determined and recorded.
>>>>
>>>> I am aware that pi-bonds are not kept recorded of, since I have no idea
>>>>
>>>> how to do that.)
>>>>
>>>>
>>>>
>>>> After the construction of graphene, I hope to merge it with some other
>>>>
>>>> membrane such as SiN. Codes are as follows:
>>>>
>>>>
>>>>
>>>> package require psfgen
>>>>
>>>> resetpsf
>>>>
>>>> readpsf $graphenePSF
>>>>
>>>> coordpdb $graphenePDB
>>>>
>>>> readpsf $sinPSF
>>>>
>>>> coordpdb $sinPDB
>>>>
>>>>
>>>>
>>>> # Write the combination.
>>>>
>>>> writepdb $finalPdb
>>>>
>>>> writepsf $finalPsf
>>>>
>>>>
>>>>
>>>> However, what I find in the final pdb is that nearly half of the
>>>>
>>>> graphene carbon atoms have been moved to the coordinate origin, i.e, (0 0
>>>>
>>>> 0).
>>>>
>>>>
>>>>
>>>> Can anyone tell me what happens?
>>>>
>>>>
>>>>
>>>> Thanks very much!
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> Ph. D Yuhui He (何毓辉)
>>> Institute of Scientific and Industrial Research, Osaka University;
>>> Mihogaoka 8-1, Ibaraki, Osaka 567-0047. JAPAN
>>>
>>
>
>
> --
> Ph. D Yuhui He (何毓辉)
> Institute of Scientific and Industrial Research, Osaka University;
> Mihogaoka 8-1, Ibaraki, Osaka 567-0047. JAPAN
>
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