On 2011-02-12 02.19, Mark Abraham wrote:
On 12/02/2011 3:45 AM, Kwee Hong wrote:
Hi Mark,
I tried but with this error:
Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491
OK. I don't know why two frames with different numbers of atoms are
written. Maybe g_confrms -one is useful. Or you can chop apart the PDB
by hand in a text editor.
Mark
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Saturday, February 12, 2011 0:01:39
*Subject:* Re: [gmx-users] doubts on g_confrms output
On 12/02/2011 2:55 AM, Kwee Hong wrote:
Hi Tsjerk,
Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?
Use trjconv -sep on the .pdb file to split it.
Mark
Regards,
Joyce
------------------------------------------------------------------------
*From:* Tsjerk Wassenaar <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Saturday, January 22, 2011 15:53:22
*Subject:* Re: [gmx-users] doubts on g_confrms output
Hi Joyce,
In pymol use 'set all_states'
Cheers,
Tsjerk
On Jan 22, 2011 8:30 AM, "Kwee Hong" <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I was trying to do some analysis following John's "GROMACS tutorial
for solvation study of spider toxin peptide".
I'm using GROMACS-4.5.3 and my command line for g_confrms is
g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
If e.g. 1OMB.pdb does not have hydrogen and md.gro does, you need to
specify two index files, pointint to e.g. the C-alpha atoms. Then the
fit can be done on these and your superposition will be fine.
The program calculated the RMSD sucessfully and fit_wet.pdb was
generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the
structure is obviously in a mess. And when I tried it out with
pymol, I can only visualised one model. Model 2 did not appear. I
wonder would it be the pdb format generated by g_confrms is not the
standard pdb format and had caused VMD and final failed to read them?
Herein, I attached part of the pdb file generated by fit_wet.pdb.
Any insight is welcomed.
Thanks,
Joyce
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