Dear Amber Community,
I have a problem with autoimage command:
I run MD simulations using script with loop that creates trajectory file (previously mdcrd, recently I switched to nc) after every ns so at the end I merge few hundreds files into one big, complete trajectory stripped off water molecules and sodium ions (script pasted in the end). The problem is I need it to be centered and for some reason autoimage command doesn't do the trick. I have pretty simple complex (protein is a homotrimer but there are no metal atoms etc and the ligand is small - 18 atoms) and my team used to use the same script for this kind of complexes more than once and it has always worked. I've tried to add anchor option to autoimage (with different anchors), use moveanchor, use image and center command instead of autoimage and nothing seems to be able center the complex properly (distances within a complex don't change but the whole complex moves like crazy). I've tried different reference files as well. And I work with CPPTRAJ: V18.01 so I don't know if this can be a version issue. There are no warning/error messages in output files. I'm completely out of ideas. Any suggestions?
Best regards,
Agata
INP=merge.sh
echo 'parm top.prmtop' >> $INP
echo 'reference ref.pdb' >> $INP
for n in `seq 3 500`;do
echo 'trajin trj.nc{val} 1 1000 50' >> $INP
sed -i "s/{val}/$n/g" $INP
done
echo 'autoimage' >> $INP
echo 'strip :WAT' >> $INP
echo 'strip :Na+' >> $INP
echo 'trajout merged.nc nc' >> $INP
echo 'run' >> $INP
cpptraj -i $INP
Agata Sowińska, PhD
Assistant Professor
Lodz University of Technology
Faculty of Chemistry
Zeromskiego 116
90-924 Lodz, Poland
www: lies.p.lodz.pl
email: agata.sowinska.p.lodz.pl
phone: + 48 42 631 3198
________________________________
[Politechnika Łódzka / Lodz University of Technology]<
https://www.p.lodz.pl>
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Received on Fri Jan 24 2020 - 09:00:02 PST
