[AMBER] Tleap is making C instaed of Cl

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 2 Feb 2017 17:09:45 +0000

Hi everyone,

i am generating parameters for my receptor and ligand complex system.

In my ligand I have Chlorine attached to it,

In my complex file I have chlorine denoted by

HETATM 22 CL1 SSS 1 31.909 25.121 -12.323 1.00 0.00 Cl

When I generate frcmod file it has

c1-c2-cl 64.929 115.520 Calculated with empirical approach

In my library file I have

 "Cl1" "cl" 0 1 131072 22 6 -0.002000

But after solvating the system when I am generating the complex pdb and viewing in chimera I cannot see green color for Chlorine, it looks like carbon. But when I see the atom nae it says Cl1.

Can any one suggest me where I am doing mistake?

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Received on Thu Feb 02 2017 - 09:30:04 PST
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