Subject: buried waters in UHBD calculations

From: Richard Greaves <[email-masked]>
Date: Thu, 02 Jan 2003 13:49:27 +0000

I am trying to run UHBD pKa calculations on a protein structure that
contains several buried water molecules. 

Whereabouts in the input coordinates should these waters appear if I do
not want to explicitly titrate them? Should they be considered as being
part of the polypeptide chain with which they are associated?

When I run these calculations UHBD outputs core files but continues to
execute ( but doesn't terminate correctly ). Could this be caused by the
waters being incorrectly set up in the calculation?
(I also get some error messages about using a non-standard floating
point mode which I have been unable to resolve)

Richard Greaves.

---

From: "Alan Leo" <[email-masked]>
Date: Thu, 2 Jan 2003 11:09:27 -0500

Hi, All:

I am using FLEXX evalution now, but when I input the ligand minimization
mol2 file,
the following error messgae is appeared:
_____________________________________________
FLEXX> lig
FLEXX/LIGAND> read TSB_min
 >> DATA ERROR: No molecules found.
    [occured in line 126 of file TSB_min]
Segmentation fault (core dumped)
_____________________________________________

I have three question:
1. I don't know if there is any newsgroup related to FLEXX except chemweb
newsgroup.

2.  The error message above point out the error of my sybyl mol2 file error,
or maybe it
is because of other reasons.

3.  Should I minimize the ligand structure before I generate the *_min.mol2
file?  Which software
I should use?

Don't peng me, I am a newbie.  :)  Your help is much appreciated..

Best,
Alan