AMBER Archive (2009)

Subject: RE: [AMBER] ACE and NME patch: VMD ???

From: Ross Walker (
Date: Tue Sep 01 2009 - 12:54:38 CDT

Hi Siddharth

Where are you getting the word 'patch' from? AMBER does not refer to
anything as a patch. This is a CHARMM'ism. What exactly are you trying to
do? Load a prmtop and save it as a psf?

To visualize things VMD should not be giving you any messages about the
bonding. It should just read what is in the prmtop and display it. For box
information this should already be present at the end of your inpcrd file. 6
floats giving X,Y,Z and the angles.

I think you need to be more explicit about what you are trying to do.

All the best

> -----Original Message-----
> From: [] On
> Behalf Of Siddharth Rastogi
> Sent: Monday, August 31, 2009 5:26 PM
> To: Amber
> Subject: [AMBER] ACE and NME patch: VMD ???
> Dear AMBER Users,
> I am using the AMBER prmtop and crd files in VMD to generate the box
> information, which can be useful in running the MD in the NAMD suite.
> However my prmtop file contains the information of ACE and NME patches,
> which is compatible with the VMD or not I dont know ?After loading the
> files VMD complains "Unusual bonding between the patch and the nearby
> residues".
> Can anyone suggest how to overcome the problem and the AMBER prmtop
> and crd
> can be used to run the MD in NAMD ?
> Your suggestions will be higly appreciated.
> --
> Siddharth Rastogi
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