Thanks David!
I tried savePdb and it all worked.
I have another question:
I have another protein, and the first 25 amino acids are unstructured, so I ran CYANA only for structured region (starting from 26th amino acid). When I want to perform a minimization, on the stage of creating prmtop and crd file I save the updated pdb file. But the problems is that in pdb file the residue number starts from 1, but it should be from 26th. Thus I can't generate RST.dist file since dist and pdb files are not compatible anymore. Is there a way to make it start count from 26nd amino acid in pdb file?
Thanks,
Olena
________________________________________
From: David A. Case [case.biomaps.rutgers.edu]
Sent: 08 February 2012 19:31
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER minimization
On Wed, Feb 08, 2012, Olena Dobrovolska wrote:
> 1. I found that instead of hydrogens it puts oxygen atoms because there
> are no N-terminal H1, H2 and H3.
OK: you have to fix this, then re-run makeDIST_RST.
>
> 2. when opened amb file in xleap these atoms are added. but after the generation of parameter files, the command
>
> ambpdb -aatm -p prmtop < P1.x > P1.amb.pdb
>
> gives me an error message 'syntax error', thus, I can't save the pdb file.
Please update to the current version of AmberTools. Or, please post your
prmtop and P1.x files, and we'll try to figure out why ambpdb is failing.
You can also use savePdb inside LEaP to create a pdb file. (If you do wnat
to upload your files, please indicate which version of AmberTools you are
using.)
>
> 3. my RST file is right,
I don't agree: your RST file is wrong, since it was made with a bad pdb file.
...dac
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Received on Thu Feb 09 2012 - 03:30:02 PST
