VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 24 2005 - 17:33:23 CDT

Hi,

So, I've tested and it seems to work. Here's my script:

package require psfgen

topology top_all22_prot.inp

segment A { residue 10 ALA }
writepdb /tmp/ala10.pdb
writepsf /tmp/ala10.psf

resetpsf

segment B { residue 20 SER }
writepdb /tmp/ser20.pdb
writepsf /tmp/ser20.psf

I'll need a complete example that demonstrates the problem to help you.

-Jim

On Mon, 24 Oct 2005, Samuel Flores wrote:

> Hi Guys,
>
> I'm having trouble with a piece of code that I thought was working. I need
> to load two separate molecules and then align them structurally.
>
> It goes something like this:
>
>> mol load pdb prot-pitch-0.pdb
>> set preprot [atomselect 0 "not water and not hydrogen"]
>> $preprot writepdb inputp.pdb
>> package require psfgen
>> topology top_all27_prot_lipid.inp
>> pdbalias residue HIS HSE
>> pdbalias atom ILE CD1 CD
>> segment U {pdb inputp.pdb}
>> coordpdb inputp.pdb U
>> guesscoord
>> writepdb input.2.pdb
>> writepsf input.2.psf
>
> This is all fine and well for the first protein. However, when further down
> in the code I issue 'resetpsf', read in another molecule, and do the same
> operation, I find that I cannot write out the second molecule. The writepdb
> command insists on writing out the first molecule! Thus it seems that even
> with resetpsf, the first molecule is in memory and the second molecule is
> just ignored. Maybe issuing resetpsf is not enough to clarify which
> molecule should be written out by the writepdb command. At any rate, could
> you advise as to correct procedure for this?
>
> Many thanks,
>
> Sam
>
>
>> ..And this was successful. Then I went to load the second protein:
>>
>>
>> mol load pdb input.pdb
>> set inputprot [atomselect 2 "not water and not hydrogen"]
>> $inputprot writepdb inputprotp.pdb
>> segment IU {pdb inputprotp.pdb}
>> coordpdb inputprotp.pdb IU
>> guesscoord
>> writepdb inputprot.2.pdb
>> writepsf inputprot.2.psf
>>
>> When I look at inputprot.2.pdb, it has TWO copies of the protein --
>> the first and the second! The first gets its coordinates zeroed out,
>> depending on whether guesscoord is used or not.
>>
>> Since the second protein loaded has twice the expected number of
>> atoms, it
>> is impossible to do a structural alignment. And yet I have to do the
>> whole
>> coordpdb and guesscoord thing because otherwise it misidentifies some
>> of the
>> atoms. Obviously when it goes through coordpdb, guesscoord, writepdb,
>> etc.
>> the second time around, it still has the coordinates of the first
>> protein in
>> memory. Can anyone tell me how to flush the first protein out of
>> memory, or
>> in some way deal with this issue?
>>
>> Thanks
>>
>> Sam
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
>> Behalf Of
>> Stanley Lan
>> Sent: Monday, October 17, 2005 5:26 PM
>> To: vmd-l_at_ks.uiuc.edu
>> Subject: vmd-l: Cannot load Gromos96 trajectory file (attached)
>>
>> Hello everyone,
>>
>> I am trying to make a movie by using the initial coordinate file and
>> the
>> trajectory file from GROMOS96 simulation result.
>>
>> Loading the coordinate file was not a problem but I couldn't load the
>> trajectory file by selecting the g96 format. VMD showed the following
>> error
>>
>> msg:
>> "No Structure information in file /<path>/<trajectory file>"
>> "ERROR) Could not read file /<path>/<trajectory file>"
>>
>> If I selected any other available formats, VMD simply showed me:
>> "ERROR) Could not read file /<path>/<trajectory file>"
>>
>> Is there a way to "turn up" the log level so that the error message
>> can be
>> more interpretable and verbose?
>>
>> I am using VMD 1.8.3 on a linux PC (slackware10.2)
>>
>> My final goal is to make a movie out of my initial coordinates and the
>> trajectory from GROMOS result.
>>
>> Thanks in advance.
>>
>> -Stanley
>>
>> Here is part of my trajectory file (I deleted a big portion of it
>> since they
>>
>> didn't seem important to me, I could be wrong. Please contact me if
>> you
>> need the complete file for testing.):
>>
>> =BOF=
>> TITLE
>> $Id: iempcl.dat,v 1.2 2000/10/20 12:29:39 gromos Exp $
>> END
>> TIMESTEP
>> 147 0.518588722
>> END
>> ENERGY
>> # ENER
>> -0.3215475E+05
>> 0.7724562E+04
>> 0.7724562E+04
>> 0.2910733E+02
>> 0.2910733E+02
>> 0.2910733E+02
>> 0.7695455E+04
>> 0.7695455E+04
>> -0.3987932E+05
>> 0.0000000E+00
>> # 10
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.2553529E+02
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.6098352E+04
>> -0.4648930E+05
>> -0.3175785E+03
>> # 20
>> 0.8036724E+03
>> 0.0000000E+00
>> # ENERES
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> 0.0000000E+00
>> # NUMUSD
>> 3
>> # ENERLJ,ENERCL,ENERRF,ENERRC
>> 0.4619526E+01 0.3951470E+03 -0.6761563E+02 0.6620401E+02
>> 0.5665094E+02 -0.2613196E+04 0.2889851E+02 0.7374684E+03
>> -0.1190074E+03 -0.9500724E+03 0.1531307E+03 0.1461857E-04
>> -0.2879240E+00 0.1225865E+03 -0.2392660E+02 0.0000000E+00
>> 0.7889620E+02 -0.8599962E+03 -0.1382724E+03 0.4296198E-06
>> 0.6077481E+04 -0.4258377E+05 -0.2697931E+03 -0.5871092E-05
>> END
>> POSITIONRED
>> 1.126477718 1.364905596 1.582740545
>> 1.274110794 1.436378002 1.588123560
>> 1.196202159 1.413280845 1.529842257
>> 1.150310636 1.494140029 1.493021369
>> 1.237280846 1.322410583 1.421857595
>> 1.116110444 1.268722653 1.345409513
>> 1.041743159 1.369518042 1.257558942
>> 1.157806635 1.148080349 1.261076927
>> 1.335683942 1.393326402 1.328620553
>> 1.447785378 1.344178796 1.316570878
>> # 10
>> 1.297751665 1.514312387 1.288480163
>> 1.203242421 1.546259999 1.295231819
>> [Deleted]
>> 2.443255663 2.409054279 2.123311281
>> 2.324791193 2.998526096 1.911451221
>> # 2830
>> 2.352324724 2.907167435 1.881488562
>> 2.311476469 2.996967316 2.010550261
>> 1.946586013 2.790724039 2.087211609
>> 1.871105909 2.766450882 2.025480032
>> 2.012133360 2.714556694 2.089403629
>> 2.275995493 2.807771683 2.853367329
>> 2.291668892 2.787541151 2.756246328
>> 2.206549168 2.744504929 2.888798475
>> END
>> BOX
>> 3.045200109 3.058700085 3.006109953
>> END
>> =EOF=
>>
>>
>
>