Hello Amber users,
I tried to introduce two non-standard residues (Octyl group: C8H17 and Methyl: CH3) to a peptide sequence in Amber following this tutorial: (http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/index.html).
I cut the Octyl and Me out of peptide separately and add Nme to them to mimic an adjacent amino acid. I calculated the charge of Octyl-Nme and Me-Nme using Gaussian program. I assigned the charges and atom types to them using antechamber in a way that total charge of each (Octyl-Nme and Me-Nme ) is equal to -1. After deleting Nme group from them, I also manually edited the charge of carbon atom in the octyl and Nme to be sure that I get -1 as the net charge for the non-standard residues as a dirty and fast solution. After defining the head and tail of the non-standard residues I save off the non-standard residue libraries. After loading all libraries, missed parameters and pdb file of the peptide including non-standard residues, there is no connection between the nonstandard residues and the standard residues of the peptide they are attached to in xleap. I connected them manually in the xleap and saveoff the toatal *.lib file. Now the total charge of the peptide is not integer.
Why I get the non-integer value for the charge of the total system after connecting non-standard residues to the structure? And how can I get rid of it?
I am a newbie in Amber. I appreciate your help and guidance.
Thank you very much.
Cheers,
Maral
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Department of Chemical and Materials Engineering
University of Alberta
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Received on Tue Mar 17 2015 - 14:30:02 PDT
