AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: Carlos Simmerling (
Date: Sun Jan 18 2009 - 07:08:41 CST

are the coordinates the same as the pdb, just incorrect bonds or
length? or are the coordinates wrong too? do all of the atoms show up
in the same locations, or are atoms moved around? check these by
loading the inpcrd/prmtop in 1 molecule and pdb in the other, and
overalpping. this will help you to troubleshoot.

On Sat, Jan 17, 2009 at 9:48 PM, David A. Case <> wrote:
> On Fri, Jan 16, 2009, Jenny Iskrenova wrote:
>> The only warning that tleap gives is about the net charge of the
>> molecule being non-zero. The structure looks fine in xleap, as well.
>> The bonds look distorted when I load acetate-vac.prmtop and
>> acetate-vac.inpcrd in VMD.
>> Would this, really, be a problem with VMD?
> Sounds like it. Did you tell VMD you have an "Amber7" prmtop file (not
> just an "Amber" prmtop)? Other than that, I don't see the problem --
> maybe someone else on the list will be able to help.
> ...dac
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