AMBER Archive (2008)

Subject: RE: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Apr 14 2008 - 16:50:27 CDT

Hi,David:

Thank you for you response. For the method to cut off some parts far
away from binding region to calculate entropy, I have been trying to
find some papers which can support this method, but I didn't find
anything. If you know some papers using this method, can you point me
out?

Thanks,

Qi

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Thu 4/10/2008 12:03 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f
 
On Wed, Apr 09, 2008, Qi Yan wrote:
>
> Maximum nonbond pairs 35934002
> ASSERTion ' ier == 0 ' failed in nmode.f at line 106.
>
>
> I checked mailing list and found some people got the same problem
> before. This belong to memory issue. In addition to increase memory,
> some people said they just cut off some parts which are far away from
> binding region or change ismem=1 in the input file without calculating
> eigenvectors.

These are all reasonable suggestions....good luck...dac

Hi,All:

I try to use nmode to calculate entropy, but I got the following error
message.

Total memory required : 970770053 real words

Total memory required : 36449606 integer words

Total memory required : 25980 4-character words

Maximum nonbond pairs 35934002
ASSERTion ' ier == 0 ' failed in nmode.f at line 106.

I checked mailing list and found some people got the same problem
before. This belong to memory issue. In addition to increase memory,
some people said they just cut off some parts which are far away from
binding region or change ismem=1 in the input file without calculating
eigenvectors.

My question is whether the above methods are reasonable. Actually, I
want to calculate the binding affinity by mm_pbsa. I have done other
parts except entropy. Does it mean the eigenvector is not necessary in
my situation? Are there some papers which just use binding region to
calculate entropy?

Thanks in advance,

Qi

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