I believe C5=C6 should be atom type cB and their respective hydrogens should be hB. You can check $AMBERHOME/dat/leap/parm/lipid14.dat to look at the atom types.
Best,
Callum
________________________________
From: Vijay Achari <glycoamber.gmail.com>
Sent: Sunday, August 12, 2018 5:58:42 PM
To: AMBER Mailing List
Subject: [AMBER] alkyl chain unsaturated bond
Dear Amber experts,
I am using AMBER14, with loading force files *leaprc.ff12SB, GLYCAM06_j, *
and* lipid14.dat*
I need some help on choosing correct atom type for carbons in aliphatic
chain with a unsaturated bond.
My aliphatic chain as below:
*-C4-C5=C6-C7-*
The *C4 & C7* are connected to two aliphatic hydrogen atoms each. *C5 & C6*
connected by a double bond and each carbon connected to a single hydrogen.
I used atom type cA for C4 & C7 carbons and hA atom type for the four
hydrogen atoms which are connected to C4 & C7.
*I am not sure what "atom type" to use for C5 & C6 which connected via a
double bond and to the respective hydrogen atoms.*
I appreciate a help for this problem.
Thanks.
Vijayan
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Received on Mon Aug 13 2018 - 07:30:07 PDT
