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
