Subject: Summary: FLEXX error message from ligand MOL2 read

From: "Alan Leo" <[email-masked]>
Date: Tue, 7 Jan 2003 11:31:38 -0500

Hi, All:

Here is summary of my question related to my questions,  thanks Holger,
Mireille, Joe 's
help.

At last,  I resolved this problem.  It is because of mol2 file error. When I
generated the mol2
file,  I should double check the file format and atom_type.   I used Babel
to generate the mol2
file from x-ray pdb file.  Don't believe in software completely, one should
double check the file
before using FLEXX.

Best,
Alan
___________________________ Original message __________________________
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 questions:
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
+++++++++++++++++ Answers +++++++++++++++++++++
Question 1:
**** From Joe
Well, I thought it was sold/supported by Tripos?  If you have it from
them, why not call Support?  If Tripos isn't involved, how about
BiosolveIT.de,
the authors...

**** From Holger
There is currently no FlexX specific newsgroup. However, please feel
free to send any comment and question to [email-masked].

Question 2
**** From Joe
How was the mol2 file created?  As I recall, FlexX is rather specific about
what it wants to see in the file, and if it's missing or not quite correct
it
might complain.  I worked with FlexX on/off for several years, and it was
rather difficult to get the program to core dump.  Can something like CORINA
read the mol2 file?  If so, have it read/write a new mol2 file to see if
anything changes (FlexX works well with Corina, I think).

**** From Mireille
When I used Flexx, I did it through the Sybyl FlexX interface.

Recently Molecular networks , group of Gasteiger, who wrote also corina,
brought out "cliff" .

**** From Holger
The error message indicates in fact an error in the mol2 file. There
 may by plenty of reasons, so that I cannot say much without the file.

Question 3

**** From Joe
It should not matter, as long as the bond lengths and angles of your input
structure are reasonable. FlexX works in torsional space, and looks to an
external program to flex rings.

**** From Mireille
yes I minimized the ligand structure before saving it to *_min.mol2. I did
this in Sybyl.

**** From Holger
Ligand structures should always be minimized before docking. You can
use any external force field for minimizing the ligands e.g. the Tripos
force filed with comes with Sybyl. Please, note that the newes FlexX
version is able to minimize ligands upon loading, if the flag
AUTOMINIZISE in the config.dat is set to 1.
++++++++++++++++++++++++++++++++++++++++++++++++++++++

Joe from [email-masked]
Mireille from [email-masked]
Holger from [email-masked]