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 ptraj.in
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 lig_en_extract.in
&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 lig_en_extract.in -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
libintlc.so.5 00002B1E31584AB1 Unknown Unknown Unknown
libintlc.so.5 00002B1E31583A85 Unknown Unknown Unknown
libifcore.so.5 00002B1E3107FB43 Unknown Unknown Unknown
libifcore.so.5 00002B1E30FF4ADE Unknown Unknown Unknown
libifcore.so.5 00002B1E30FF4286 Unknown Unknown Unknown
libifcore.so.5 00002B1E31023576 Unknown Unknown Unknown
libifcore.so.5 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
libc.so.6 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 - 10:30:03 PDT
