AMBER Archive (2007)

Subject: RE: AMBER: perturbed atoms are not bonded on using TIP5P wate

From: sugino tatsuro (tsugino_at_comas.frsc.tsukuba.ac.jp)
Date: Tue Jan 16 2007 - 23:47:51 CST

Dear David,

 

Thank you very much for your advices:

> It looks like a weird bug in LEaP. If you really need to do this
particular

> calculation, you might have to upgrade to Amber 9 (which doesn't use

> perturbed prmtop files any more).

 

Still by using AMBER8, I compared two types of files, each of which is in
the

presence or absence of perturbation. As a result, in the file including
perturbation

the bond information was lost. So, I transferred the lost (bond) information
parts

toward the file including the perturbation. But I detected the following
error in the

initial phase of the sander calculation;

 

EXTRA_PTS: too many nghbrs

 

I searched AMBER Archive, and found the a related issue as follows;

http://structbio.vanderbilt.edu/archives/amber-archive/2004/2039.php

 

According to it, I should modify a file of "extra_pts.f" for TIP5P. But I
cannot

see further detailed information for the modification in the Arichive. So,
if you

would you tell me how to rewrite the program in the case of the TIP5P water

model, I would much appreciate it.

 

Thank you very much in advance for your help.

 

best regards,

Sugino

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu