Re: [AMBER] Problem when calculating MMPBSA (Jason Swails)

From: dongying0512 <>
Date: Mon, 30 Dec 2013 09:21:37 +0800 (CST)

Hi Jason,
Thank you very much for your reply. I applied all updates and recompiled AmberTools 13 and I still got the same problem. All of the input files and results are attached here and I'm sure you can reproduce the error.
Thanks again
Dong Ying

>Message: 8
>Date: Fri, 27 Dec 2013 02:03:35 -0500
>From: Jason Swails <>
>Subject: Re: [AMBER] Problem when calculating MMPBSA
>To: AMBER Mailing List <>
> <>
>Content-Type: text/plain; charset=ISO-8859-1
>On Fri, Dec 27, 2013 at 1:50 AM, dongying0512 <> wrote:
>> Hi all,
>> I have a problem when calculating MMPBSA, and i'm not sure where this
>> error is coming from. Please help me out. Thamks in advance.
>> And all of the nput files and results are attached.
>> dy.ubuntu:~/Work$ $AMBERHOME/bin/ -O -i -o RESULT.dat
>> -sp DNA_AMP_wb_vmd.prmtop -cp DNA_AMP_ante.prmtop -rp DNA_ante.prmtop -lp
>> AMP_ante.prmtop -y test.dcd
>> Loading and checking parameter files for compatibility...
>> sander found! Using /home/dy/amber12/bin/sander
>> cpptraj found! Using /home/dy/amber12/bin/cpptraj
>> Preparing trajectories for simulation...
>> 10 frames were processed by cpptraj for use in calculation.
>> Running calculations on normal system...
>> Beginning PB calculations with /home/dy/amber12/bin/sander
>> calculating complex contribution...
>> calculating receptor contribution...
>> calculating ligand contribution...
>> ValueError: could not convert string to float: EEL
>> Exiting. All files have been retained.
>This is very strange. Please make sure you have applied all updates (and
>recompiled AmberTools 13). If you are still getting this error, can you
>create a tarball of the necessary topology files and a trajectory file with
>2 snapshots so I can try to reproduce this error? You can send me the
>files off-list.
>Jason M. Swails
>Rutgers University
>Postdoctoral Researcher

>AMBER mailing list
>End of AMBER Digest, Vol 717, Issue 1

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Received on Sun Dec 29 2013 - 17:30:02 PST
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