AMBER Archive (2004)

Subject: Re: AMBER: Using TIP4P water in free energy calculation

From: David A. Case (
Date: Fri Aug 06 2004 - 10:56:46 CDT

On Thu, Aug 05, 2004, Lijiang Yang wrote:
> > Can you explain what you mean by "the bonds disappeared"? Did the
> atoms fly apart?
> Yes, what I mean is that the atoms fly apart.
> Thank you for your suggestion. Here is the information I got from rdparm:
> 1.
> 2.TIP4P
> RDPARM MENU: bonds :1
> RDPARM MENU: bonds
> :1
> Mask [:1] represents 14
> atoms Mask [:1] represents
> 14 atoms
> Bond Kb Req atom names (numbers)
> Bond Kb Req atom names (numbers)

It is very hard to follow what you are posting (maybe your mail program is
mangling the output), but it looks like you have no bonds present in residue
1. This would explain why the atoms fly apart. If you edit your residue
in xleap, you should see the bonds (if they are there). The "desc" command
in LEaP can also give you information about bonds. You need to try to figure
out what you did to end up with a residue with no bonds. Try making an
ordinary (nonpert) prmtop file corresponding to the lambda=0 state, and see
if you can get that to work.

You seem to have pertbonds but no regular bonds.

...good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to