Re: [AMBER] Amber: saveamberparm error

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From: Karan Mehra <kkm7r.virginia.edu>
Date: Wed, 11 Aug 2010 15:38:11 -0400

These are the exact commands that I ran with sleap:

$sleap
[gtkleap]$ source /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
[gtkleap]$ set default fastbld on
[gtkleap]$ ctx = loadpdb ctx.pdb
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
[gtkleap]$ saveamberparm ctx ctx.prmtop ctx.crd
Error: can't find parameter for bond CT-O

Also I loaded parm99.dat and frcmod.ff99sb for force field parameters.

Thanks,
Karan Mehra
Chemical Engineering
University of Virginia 2012

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chemical/x-pdb attachment: ctx.pdb

Received on Wed Aug 11 2010 - 13:00:04 PDT