AMBER Archive (2004)

Subject: Re: AMBER: (no subject)

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 30 2004 - 15:42:15 CDT

On Fri, Jul 30, 2004, Ross Walker wrote:
>
> The problem is with the hydrogen's in your pdb file. Yours have the name
> format:
>
> xHAx whereas xleap expects the format HAxx. Hence any hydrogen that starts
> with a number instead of an H is being duplicated by xleap.

I don't think the above explanation is correct. LEaP is perfectly hapy with
the Brookhaven scheme of mangling hydrogen atom names. To my eye, the "problem"
is that most NMR file in the PDB do not use IUPAC nomenclature, but Amber
does. Here's what I did to convert the nomeclature:

protonate -keep < nmr.1.pdb > nmr.1a.pdb

This points out 1 problem about trying to figure out what the protonation
state of one of the histidines is. You could fix that (by editing the file)
or just accept the default used by Amber.

Then tleap runs just fine for me:

source leaprc.ff94
x = loadpdb nmr.1a.pdb
...<add disulfide bonds here, etc.>
saveamberparm x prmtop prmcrd
quit

Ross' alternative (removing all of the hydrogens and having LEaP add them
back in) will also work, and maybe is simpler than the above.

Generally, when you get "lots of errors from LEaP", don't be dismayed, but
look at the first one, and see if you can figure out how to get around it.
The many additional errors may then disappear as well.

...good luck...dac

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