[AMBER] T.I. - single topology HIP <-> HIE

From: Andrew Schaub <aschaub.uci.edu>
Date: Tue, 21 Nov 2017 08:53:39 -0800

Good Morning,

I'm in the process of setting up a single-topology T.I. simulation with the
HIP and HIE residues. The only difference between the two residues is the
atom name HD2 (for the protonated delta nitrogen). It looks like I need to
create a non-standard HIP residue, with the HD2 atom at the very end of the
residue? So I won't be able to use the HIP residue that comes standard in

Step 1 - Using the leaprc.protein.ff14SB in tleap, save mol2 and PDB
versions of HIE and HIP residues. close tleap.

Step 2 - In a text editor, I move HD2 to the bottom of the PDB file. So my
HD2 atom is last. I also rename the residue to something unique like MHP. I
open up a new instance of tleap, and load the MHP residue, and save as mol2.

Step 3 - Write a script to copy partial cahrges of the original HIP residue
(mol2) that I created in step 1, to the new residue MHP.

Step 4 - New tleap. Modify the 1b_leap.sh script from the tutorial:

# create a template for HIP maximally mapped to HIE
source leaprc.ff14SB
MHP = loadmol2 MHP.mol2

set MHP restype protein
set MHP head MHP1.N
set MHP tail MHP.1.C
set MHP.1 connect0 MHP.1.N
set MHP.1 connect1 MHP.1.C

saveoff MHP MHP.lib


This should give me my non-standard HIP for single-topology T.I. Now I just
need to take my original PDB of my receptor, and create two versions. One
will have a HIE residue, the other will have the new MHP residue.

Is this the standard way of doing this? It seems like a lot of work. I just
want to make sure I'm setting this up right. Any informaiton/guidance you
can provide would be appreciated.

I also understand, that HIP and HIE are not the same charge, so I'll need
to take that into account.

Best Regards,

Andrew Schaub
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Received on Tue Nov 21 2017 - 09:00:01 PST
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