Thanks Carlos, I am now able to create the prmtop and inpcrd files I needed "successfully". At least I hope so. Before I was not able to create these files. It would always give errors in Xleap and they would not be generated.
-----Original Message-----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, June 4, 2020 12:13 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] help with building an amino acid based surfactant molecule
Carefully check the parmchk2 step, and maybe look at the output it creates
On Thu, Jun 4, 2020, 1:12 PM Billiot, Eugene <Eugene.Billiot.tamucc.edu>
wrote:
> I have tried that before and loaded the frcmod file while I was in
> Xlaep but to be honest I have tired so many things I may not have used
> that correctly. I will try that again and try to follow the steps in
> the TUTORIAL B5 - Simulating the Green Fluorescent Protein using it as
> a guide. Hopefully I can get it to work. Thanks
>
>
> -----Original Message-----
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, June 4, 2020 11:52 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] help with building an amino acid based surfactant
> molecule
>
> 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.
> >> >>
> >> >>
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Received on Thu Jun 04 2020 - 16:00:01 PDT
