AMBER Archive (2009)

Subject: Re: [AMBER] Problem reading PDB file into XLEAP

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Mar 27 2009 - 07:39:26 CDT

On Thu, Mar 26, 2009, Hopkins, Robert wrote:
>
> After I loaded a DNA file (DDIRinmin.pdb) into Xleap (Amber Tools 1.2)
> from Amber 9, it was solvated, counterions were added and a new PDB
> file (IR_sol.pdb) was created. I then edited the new file in order to
> remove the last water molecule from the file using Xemacs while keeping
> the same file name. This edited file was then loaded into Xleap once
> again in order to create .prmtop and .inpcrd files, but none of the
> residues are being recognized in Xleap, as indicated in the leap.log.
> And, although .prmtop and .inpcrd files are created, these files do not
> function properly when used with sander.

It looks like your leap.log file leaves out the beginning part of the
second leap run (with the modified pdb file)(?) I don't see where the
leaprc file is being processed.

You can ignore the "not found in name map" lines...I don't know why
these are still being printed.

I don't see any obvious problems with your files. I'd suggest trying it
again(!), and seeing what sleap does.

...dac

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