Hi Eugene,
did you do the parmchk2 step of the GFP tutorial? What did it do? This is
the part that will try to guess your cross terms.
At this point, we have our residue library containing the charges for the
atoms in our modified amino acid . We next need to check that the covalent
parameters (bonds, angles, and dihedrals) that will be needed are
available. The *parmchk2* program figures out what parameters will be
needed and checks to see if they are in the standard files. If not, it
tries to make educated guesses, and puts these new parameters into a file
we are calling "frcmod.cro" here.
On Thu, Jun 4, 2020 at 11:56 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> no - unless you have all upper case (protein force field) or all lower
> case (gaff), you will need new mixed terms to cross the boundary.
>
> On Thu, Jun 4, 2020 at 11:29 AM Billiot, Eugene <Eugene.Billiot.tamucc.edu>
> wrote:
>
>> Carlos,
>> I am not sure if I understand your suggestion , can I simply change the
>> gaff atom type names associated with the errors to protein associated atom
>> type names (upper case) like those associated with amide bonds in
>> proteins?
>>
>> -----Original Message-----
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Sent: Thursday, June 4, 2020 10:22 AM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] help with building an amino acid based surfactant
>> molecule
>>
>> Sorry forgot to add thst this is usually done by manually creating the
>> needed terms, taking the force constants from gafd by analogy and changing
>> the atom types to those in the protein model (upper case).
>>
>> On Thu, Jun 4, 2020, 11:20 AM Carlos Simmerling <
>> carlos.simmerling.gmail.com>
>> wrote:
>>
>> > 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
>> > <Eugene.Billiot.tamucc.edu>
>> > wrote:
>> >
>> >> 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.
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2020 - 10:00:02 PDT
