Thank you for your reply. I have tried many different ways in order to hopefully determine the cause of this result, including non-parallel runs as you suggested. From what I have found, it seems to be involved with an inhibitor containing a nitrile group.
I have attached all the appropriate input files (over 2 emails) of which I made use of the ff99SB and gaff force fields.
Any insight as to why this simulation will run in version 10 but not in 11 would be of greatly appreciated.
Thank you,
Melissa
---------------------------------------------
Melissa Buskes
PhD student
Department of Chemistry | School of Molecular Science
La Trobe University
------------------------------
Message: 11
Date: Wed, 9 May 2012 11:47:58 +1200
From: Ben Roberts <ben.roberts.geek.nz>
Subject: Re: [AMBER] Sander Error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <A1D901F9-8DA8-42C9-A5D5-20CC9D73DAEB.roberts.geek.nz>
Content-Type: text/plain; charset=us-ascii
Hi Melissa,
Perhaps you missed Dave Case's response to your earlier copy of this email, that should have arrived overnight. Here it is again:
(quoted)
Odd. I'd first do non-parallel runs (for just a few steps) to see if the
problem is related to the parallel implementation. Also try pmemd to see if
what results that gives (again, just for a few steps).
I'm suspecting that you will have to post your files so that someone can try
to reproduce the problem.
....dac
On 9/05/2012, at 11:19 AM, Melissa Buskes wrote:
>
>
>
> Hello,
>
> I am currently attempting to run a minimisation of a complex (Inhibitor and protein) using Sander. I have been having problems running this on AMBER 11 with the following output files displaying this "error":
>
> | Local SIZE OF NONBOND LIST = 4301123
> | TOTAL SIZE OF NONBOND LIST = 16457817
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -Infinity NaN 1.7578E+06 O 1901
>
> BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6339
> VDWAALS = 214218.6554 EEL = -113699.4160 HBOND = 0.0000
> 1-4 VDW = -Infinity 1-4 EEL = -Infinity RESTRAINT = 0.0000
>
> I then resubmitted the jobs on AMBER 10 and the jobs appeared to run fine. This is the same component of the output file:
>
> Local SIZE OF NONBOND LIST = 4299672
> | TOTAL SIZE OF NONBOND LIST = 16453545
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 9.1094E+05 5.2338E+04 1.1077E+07 HB3 1874
>
> BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6340
> VDWAALS = 1000086.7124 EEL = -113709.9625 HBOND = 0.0000
> 1-4 VDW = 1382.9392 1-4 EEL = 15352.7435 RESTRAINT = 0.0000
>
> Is there maybe something that I have overlooked in regards to differences between AMBER 10 and 11? As I am using the exact same input files in both cases.
>
> Initially, I thought this result may have been an issue with clashing atoms, but I have since checked and resolved that these do not exist anymore.
>
> Any help/ suggestions would be much appreciated,
>
> Thank you,
>
> Melissa
>
>
>
>
>
>
>
>
>
>
>
>
>
> ---------------------------------------------
> Melissa Buskes
> PhD student
> Department of Chemistry | School of Molecular Science
> La Trobe University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Jun 22 2012 - 01:30:03 PDT
