Hi I have posted similar error recently. However, I believe there is no
immediate solution for it. This is becuase you system probably has more than
4000 atoms (It is clearly mentioned in amber manual). I solved my problem by
by cutting out many/some of the residues (mostly at loop area) far from the
ligand. Of couse one needs to add C/N-terminal atoms. YOu may require to
minimize the system bit longer.
I hope it may help you,
Best wishes,
----- Original Message -----
From: "Cenk Andac" <cenk_andac.yahoo.com>
To: <amber.scripps.edu>
Sent: Sunday, February 26, 2006 6:26 PM
Subject: Re: AMBER: dynamic memory allocation problem in nmode
> In addition to my previous message, I have also tried
> ismem=1 in my nmode input. However, ismem=1 did not
> work either.
>
> ..waiting for a solution to this.
>
> regards,
>
> jenk.
>
> --- Cenk Andac <cenk_andac.yahoo.com> wrote:
>
>> Dear amber community,
>>
>> I have been running entropy analysis for MD
>> snapshots
>> of a 54 KDa system (receptor+ligand) by the mm_pbsa
>> module of amber8. After sander minimization of the
>> system, the nmode analysis of the first snapshot
>> fails
>> giving the following error message.
>>
>>
>>
>> Total memory required : 423592059 real words
>>
>> Total memory required : 23938104 integer words
>>
>> Maximum nonbond pairs 23505795
>> ASSERTion ' ier == 0 ' failed in nmode.f at line
>> 105.
>>
>>
>> As far as I know this message pops-up when there is
>> something wrong with dynamic memory allocation in
>> nmode. Could anyone of you know know how to
>> troubleshoot this problem?
>>
>> regards,
>>
>> jenk.
>>
>>
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Received on Sun Mar 05 2006 - 06:10:05 PST
