AMBER Archive (2008)

Subject: RE: AMBER: MM_PBSA binding error

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Tue Nov 04 2008 - 13:18:54 CST

Hi Larry,

It's is "is_init.f"

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Larry Layne
Sent: Tuesday, November 04, 2008 5:51 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: MM_PBSA binding error

Ray, (or anyone for that matter)
I am unable to find the pb_init.f file in my amber9 install directory. Can
you tell me where exactly it is located?

Thanks,
Larry

> Larry,
>
> If that's the case, please insert the additional keywords "fillratio =
> 3.0" to your pbsa input file to change the default value. It has been
> asked and answered before on the mailing list on how to revise the perl
> script so you can get it inserted automatically into the input file ...
>
> All the best, Ray
>
> On Fri, Oct 31, 2008 at 5:56 AM, Larry Layne <llayne_at_andrew.cmu.edu>
> wrote:
>> Ray,
>>
>> I checked my out file for that ligand and sure enough, there is an
>> error. It reads:
>>
>> PB Bomb in setgrd(): focusing grid too large 2 reset fillratio to a
>> larger number 2.000.
>>
>> I've attached the output file. I'm not sure what that means or how to
>> remedy the problem. Is it saying the grid I am suing to do the PBSA
>> calculation is too large? Any suggestions would be helpful.
>>
>> Thanks, Larry
>>
>>
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