Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library?

From: Cruzeiro,Vinicius Wilian D <>
Date: Thu, 19 Oct 2017 14:28:38 +0000

Hello Michael,

Parmed is able to remove atoms (strip command) and also change atomic charges (change CHARGE command), however it seems to me you are having problems on the new SER bond as you are dealing with a complex of serine protease, correct? You have to take a look at the atom types of the angle tleap is complaining about and then make sure the force field parameters for it are listed on your frcmod file. If you are not sure what parameters to provide, in situations like this people generally look at other systems that have a similar bond to the one you need and copy the parameters from there.

I hope this helps.


Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

From: Michael Shokhen <>
Sent: Thursday, October 19, 2017 8:42:38 AM
Subject: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library?

Dear Amber experts,

Several days ago I have sent email to the AmberList asking for help with Amber tutorial A1
aimed at the addition of a non-standard amino acid residue to the Leap library.
My non-standard residue is SER with deprotonated O gamma atom.
I need to use this SER with anionic side residue O- atom in my MD simulations
of Michaelis complex of serine protease with substrate in frames of Amber16 ff14SB force field.
The previously reported problem was about the xleap graphical Table opening needed for
the setting of the RED generated atomic charges.
Prof. Case has kindly answered my question. He advised me to check that NumLock is
not set ON in my Linux system. That was indeed the situation – NumLock was set ON.
When I set it OFF the Xleap opened the Table for settings of the atomic charges of the
residue in question. Anyway, the Xleap didn’t transfer previously defined in Xleap the
inter-atomic connectivity data and by RED generated atomic charges to the lib file.
Working the problem around I have added manually directly to the lib file the missed charges
and the connectivity data between residue atoms. Nevertheless, I have failed to get
the parameters prmtop file for my non-standard residue. Tleap has reported that some
angle parameters are absent. I have examined and compared the structure of the lip file
of my non-standard deprotonated SER residue with the standard SER residue in the
amber/dat/leap/lib/amino14ipq.lib file. The architecture of my lib file was identical to the standard one.
In fact, he reported by tleap missed angle parameters are not collected in the lib file generated
following the A1 tutorial. The angle parameters are collected in the amber/dat/leap/parm directory files.
Unfortunately, the A1 tutorial says nothing how to define such parameters for the non-standard residue.
I think that the only way for me to resolve the problem with the deprotonated ionized SER is the direct
addition this non-standard residue to the parameter libraries of the ff14SB force field.
Unfortunately, I don’t know how to do this.
Amber manual does not contain any practical protocol illustrated by clear and detailed examples for doing this.
I would appreciate if you will address me to any detailed protocol relevant to my task.

Many thanks,

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Received on Thu Oct 19 2017 - 07:30:03 PDT
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