Re: [AMBER] Developing Parameters using tleap

From: David A Case <>
Date: Sat, 23 May 2015 12:29:33 -0400

On Fri, May 22, 2015, Brittany Boykin wrote:
> I am trying to start QM/MM setup/simulation for already simulated system
> (H293S-Arg) using the cluster analysis pdb, cluster_4. I am currently
> at the developing parameters for the complex but have stumbled upon a
> slight problem. I ran this pdb (B4M_initial_str_cluster_9-SAM-fixed.pdb)
> through tleap and its giving me the following error:
> See below for leap.log file:

What leaprc file(s) did you load?

I found it hard to understand the remainder of your problem. If you are
going to start QM/MM for an "already simulated system", you should not need to
re-run tleap. The only place a QM/MM simulation differs from an MM simulation
is in the sander input.

You error messages all look like ones involving standard amino acid residues.
Make sure you can correctly run tleap on a simple protein (no "complex", no
non-standard residues). Then build you way up to more complex systems.

...good luck....dac

AMBER mailing list
Received on Sat May 23 2015 - 09:30:02 PDT
Custom Search