1. I found that instead of hydrogens it puts oxygen atoms because there are no N-terminal H1, H2 and H3.
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.
3. my RST file is right, though for its generation I use .amb file that has no N-term H1,H2, and H3. (since I can't create pdb using ambpdb command).
What is the right syntaxis for ambpdb command to save the pdb file right after addition of these hydrogens?
________________________________________
From: David A. Case [case.biomaps.rutgers.edu]
Sent: 08 February 2012 14:38
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER minimization
On Wed, Feb 08, 2012, Olena Dobrovolska wrote:
>
> but it already stands LISTIN= POUT in sander run.
> My output file doesn't correspond to RST file. So My guess something
> happends during minimization. Can you please take a look?
It looks like something went wrong when you created the RST file. The very
first restraint connects atoms 25 and 41. The comments indicate that these
are hydrogens; but the actual atoms involved include an oxygen atom. Sander
doesn't look at the comments, just at the actual atom numbers. So you need to
try to figure out what went wrong at the makeDIST_RST step. Make sure that
the pdb file you used at that step exactly matches the prmtop file: e.g. use
ambpdb to create the input pdb file for makeDIST_RST.
...good luck...dac
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Received on Wed Feb 08 2012 - 10:30:03 PST
