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

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Thu, 19 Oct 2017 14:27:17 +0000

Dear Carlos,



Many thanks for quick response.

Am I right that you are asking, if in my MD simulations

I use the ff14SB force field or ff14ipq force field?

I use the ff14SB force field in frames of amber16.

I have mentioned in my email the amber/dat/leap/lib/amino14ipq.lib file

because that was the only leap library file for standard SER I could identify
in order to verify my lib file generated by xleap for the deprotonated SER
following the orders of the A1 tutorial.

I couldn't find amber/dat/leap/lib/amino14.lib file in order to the above mentioned
libraries comparison.


Michael





*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, October 19, 2017 4:46:13 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library?

Just a quick question to better understand how to help - are you using
ff14SB or ff14ipq? These are not the same, and maybe you modified the wrong
file. They also may have different needs in terms of matching atom types.

On Oct 19, 2017 8:43 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
wrote:

> 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 Ė 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 didnít 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 donít 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,
> Michael
>
>
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 19 2017 - 07:30:03 PDT
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