[AMBER] Problem in protonating.

From: Harshala Haldankar <harshala7h.gmail.com>
Date: Fri, 13 Mar 2015 16:46:02 +0530


I am new to Amber software and want to simulate a* helical peptide *in
water. I am trying to protonate my peptide in xleap using following command:

protonate -k -d $AMBERHOME/dat/PROTON_INFO -i pcpep_cap1.pdb -o pc_prot.pdb
-l pcprot.out

and i tried this also

$AMBERHOME/exe/protonate -k -d $AMBERHOME/dat/PROTON_INFO -i pcpep_cap1.pdb
-o pc_prot.pdb -l pcprot.out

but am getting syntax error.

What should i do?
please help.
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Received on Fri Mar 13 2015 - 04:30:03 PDT
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