Re: [AMBER] help with building an amino acid based surfactant molecule

From: Carlos Simmerling <>
Date: Thu, 4 Jun 2020 11:20:24 -0400

It looks like you're missing the cross terms between gaff and the protein
force field. This would be expected when you combine 2 force fields in the
same molecule, which is what you said you want to do so at least part part
seems to have gone properly. Next you would need to prepare those boundary
terms manually, I am not aware of a tool to do it (others on the list may
have tools....). In general combining 2 force fields is a more advanced
method since they don't know how to talk to each other at the boundary.

On Thu, Jun 4, 2020, 11:01 AM Billiot, Eugene <>

> Hello Folks,
> I have been struggling for over a month to build an amino
> acid-based lipid with undecanal as the hydrophobic tail and the carbon on
> the C=O group of the undecanal forming an amide bond with the first amino
> acid in my dipeptide based surfactant. When I run antechamber on my
> surfactant molecule, it replaces amino acid force field parameters with
> gaff forcefield parameters and it converts all of the residues (such as
> und-LEU-VAL) with und being the undecanal group to one residue (the first
> one - und) losing the amino acid residue information.
> I do not want to use gaff forcefield parameters for the amino acid
> head groups because I suspect the protein database forcefields are better
> descriptors. How can I build the surfactant molecule with three residue
> names such as described above (und-LEU-VAL) with und described by the gaff
> forcefield parameters and the amino acid moieties described by the protein
> forcefield parameters? Every time I build the sequence in Xleap and try to
> run "saveamberparm" I get the errors below which are related to the amide
> linkage between the C=O on the undecanal forming an amide bond with the
> first amino acid in my dipeptide based surfactant (Leucine in the example I
> mentioned).
> The problem is that I am somewhat of novice in terms of
> computational chemistry. The one Amber tutorial that I found most useful
> is TUTORIAL B5 - Simulating the Green Fluorescent Protein. I feel
> confident that the answer to my problem lies in that tutorial, but I get
> lost in trying to understand what the most relevant points are in helping
> me address my problem. Any help would be greatly appreciated. Thanks!!!!!
> NOTE: In case it is not clear, when I create my undecanal-LEU-VAL sequence
> in Xleap, I named it ULV, thus the three-letter abbreviation (ULV) below.
> > saveamberparm ULV ULV.prmtop ULV.inpcrd
> Checking Unit.
> Warning: The unperturbed charge of the unit (-1.000000) is not zero.
> Note: Ignoring the warning from Unit Checking.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Error: Could not find bond parameter for: c - N
> Building angle parameters.
> Error: Could not find angle parameter: o - c - N
> Error: Could not find angle parameter: c - N - H
> Error: Could not find angle parameter: c - N - CX
> Error: Could not find angle parameter: c3 - c - N
> Building proper torsion parameters.
> Error: ** No torsion terms for o-c-N-H
> Error: ** No torsion terms for o-c-N-CX
> Error: ** No torsion terms for c3-c-N-H
> Error: ** No torsion terms for c3-c-N-CX
> Building improper torsion parameters.
> old PREP-specified impropers:
> <und 1>: C10 H34 C11 O12
> total 5 improper torsions applied
> 1 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Warning: Parameter file was not saved.
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Received on Thu Jun 04 2020 - 08:30:02 PDT
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