Re: [AMBER] problem with extraction of potential energy for the ligand

From: Bill Ross <>
Date: Sun, 07 Jun 2015 14:20:28 -0700

Interestingly it is having a problem reading your -
was there no other info after the stack trace to indicate what line of
the file is involved? Could there be Windows line endings in the file?

Aside from that issue, I see nothing that directs sander to read the
trajectory file - note that with -O plus -c lig.traj you could expect
the file to be truncated, if -c is still an output file specifier. I
believe sander may have an option to read an mdcrd and calculate
energies - note that it would require a prmtop for the ligand rather
than the complex, in case que.prmtop refers to complex below.


On 6/7/2015 10:14 AM, Maryam Hamzehee wrote:
> Dear Amber List
> I am trying to extract potential energy for my ligand from the ligand-receptor complex during the MD simulation (1ns). I have extracted the trajectory file of the ligand from ligand-receptor complex using ptraj, the input file is as follows:
> [maryam.cluster quercetin]$ more
> trajin md.binpos
> strip_mask :1-1330
> trajout lig.traj nobox
> #rms first out ligandrmsd.txt :1331
> #average ligaverage.pdb pdb :1331
> For extraction of potential energy I used the following input file:
> [maryam.cluster quercetin]$ more
> &cntrl
> imin=5,maxcyc=1,
> cut=8.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=0,
> /
> But the following error has been observed:
> [maryam.cluster quercetin]$ /share/apps/amber11/exe/sander -O -i -o lig_en_extract.out -p que.prmtop -c lig.traj -y que.inpcrd
> forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
> Image PC Routine Line Source
> 00002B1E31584AB1 Unknown Unknown Unknown
> 00002B1E31583A85 Unknown Unknown Unknown
> 00002B1E3107FB43 Unknown Unknown Unknown
> 00002B1E30FF4ADE Unknown Unknown Unknown
> 00002B1E30FF4286 Unknown Unknown Unknown
> 00002B1E31023576 Unknown Unknown Unknown
> 00002B1E31021085 Unknown Unknown Unknown
> sander 00000000004EFF34 Unknown Unknown Unknown
> sander 00000000004AF671 Unknown Unknown Unknown
> sander 000000000048C7B5 Unknown Unknown Unknown
> sander 000000000048C60C Unknown Unknown Unknown
> sander 0000000000402DEC Unknown Unknown Unknown
> 0000003C0021D994 Unknown Unknown Unknown
> sander 0000000000402CF9 Unknown Unknown Unknown
> How can I extract the potential energy for the ligand. I would be grateful if you could kindly help me in this regard.
> Any help in this regard would be highly appreciated.
> All the bestMaryam
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Received on Sun Jun 07 2015 - 14:30:02 PDT
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