AMBER Archive (2004)

Subject: Re: Re: Re: AMBER: Why the surface calculations sometimes fail?

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Wed Dec 15 2004 - 22:12:59 CST


Dear David A. Case,

        Sorry for the delay. Please find enclosed as attachment the requested parmtop file.
Actually,even the surface calculation of receptor fails sometimes.
Thanks in advance.

======= 2004-12-13 18:29:00 you wrote£º=======

>On Thu, Dec 09, 2004, hj zou wrote:
>>
>> Please find enclosed as attachment the log file and pdb.
>> This is the ninth complex snapshot extracted from trajectory.
>> The calculation of surface area of this snapshot failed while that of
>> the previous eitht snapshots worked well.
>
>Can you provide the prmtop (or the pqr file) that you actually used...the
>problem may arise with the radii or coordinates of the ligand.
>
>....dac
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

= = = = = = = = = = = = = = = = = = = =
                        
************************************************
Hanjun Zou
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel£º +86-21-50806600-1201
E-mail: hjzou_at_mail.shcnc.ac.cn
************************************************



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