yes please look at that paper. there is no reason to work on implementing
that old force field since the current ones work well for folding that
system.
On Tue, Mar 10, 2020 at 1:27 PM ankita mehta <mehtaroadies.gmail.com> wrote:
> Sir,
> Thanks for the reply.
> 1. We are trying to do similar to that one for the time being.
> I will also see the paper you recommended.
> Is this the latest paper for studing protein folding through MD or are
> there further advancements also.
>
> 2. How to read frcmod file that you get when u run parm command in parmed.
> I want to check whether modified force field had been utilised or not.
>
> 3. I am getting some warning when I load modified FF as follows:
>
> Improper torsion lines
> I want to correct this warning...
>
> TIA!
>
> On Mon 9 Mar, 2020, 10:15 PM Carlos Simmerling, <
> carlos.simmerling.gmail.com>
> wrote:
>
> > maybe you could tell us a little more about what you're trying to do.
> That
> > is a very old force field. Do you need that specific one, or do you want
> to
> > do similar work? You might take a look at this paper instead, it has the
> > same protein included but also many more, and is a modern force field and
> > solvent model that can be accessed in the standard Amber release.
> > https://pubs.acs.org/doi/abs/10.1021/ja5032776
> >
> > --
> > Carlos Simmerling, Ph.D. (he, him, his)
> > Marsha Laufer Endowed Professor of Physical and Quantitative Biology
> > Professor, Department of Chemistry
> > Associate Director, Laufer Center for Physical and Quantitative Biology
> > Room 119 Laufer Center, Stony Brook University, Stony Brook, NY
> 11794-5115
> >
> > http://www.simmerlinglab.org
> >
> >
> > On Mon, Mar 9, 2020 at 12:40 PM ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> >
> > > Hiii,
> > > 1. I have run the above command . And i got the name.frcmod file.Which
> I
> > am
> > > attaching here below.
> > > How to interpret this file so that i get to know parameters are taken
> > from
> > > which file ?
> > >
> > > 2.I am attaching the pdf format of modified parameters file in this
> mail.
> > > I don't see any specification of angle and dihedral angle category.
> > > Can you guide me for the same.
> > > How to look for them?
> > >
> > > TIA!
> > >
> > >
> > >
> > > On Mon, Mar 9, 2020 at 3:53 AM Kellon Belfon <kellonbelfon.gmail.com>
> > > wrote:
> > >
> > > > 1. I think the order you have is correct. The parameters in your
> > modified
> > > > leaprc (leaprc.ff101) should overwrite any similar definition in the
> > > ff99SB
> > > > leaprc, if it is loaded after the ff99SB leaprc. To double check if
> you
> > > > have the right parameters you can use parmed.
> > > >
> > > > parmed topology_file
> > > > writeFrcmod name.frcmod
> > > >
> > > > Then you can look at the name.frcmod file to see if it have the
> > > parameters
> > > > you intend to use.
> > > >
> > > > 2. The warning is letting you know that you did not define enough
> > > > parameters for an Improper dihedral. Which leads me to ask this
> > question.
> > > > Which section of the file, loaded by loadAmberParams do you have the
> > > > definition for HW OW HW? Is it under IMPROPER or ANGLE? It should be
> > > under
> > > > the ANGLE section.
> > > >
> > > > On Sun, Mar 8, 2020 at 1:59 PM ankita mehta <mehtaroadies.gmail.com>
> > > > wrote:
> > > >
> > > > > Thanks for the reply .
> > > > > I managed to correct the formatting.
> > > > > Now, I am having following concerns.
> > > > > 1. I have two files from which parameters can be loaded .
> > > > > One is leaprc.ff99SB and other one is modified leaprc.ff101.
> > > > > Now, how to be sure that amber parameters of modified parameters
> will
> > > be
> > > > > loaded.
> > > > > Is there any connection in what order i write them in tleap , that
> > > order
> > > > > it reads the parameters.
> > > > >
> > > > > 2. I am having some warning after loading the both parameters
> files:
> > > > > Improper torsion lines
> > > > > : what to do to correct this warning?
> > > > >
> > > > > Thanks!
> > > > >
> > > > >
> > > > >
> > > > > On Fri, Mar 6, 2020 at 6:30 PM David A Case <
> david.case.rutgers.edu>
> > > > > wrote:
> > > > >
> > > > > > On Fri, Mar 06, 2020, ankita mehta wrote:
> > > > > >
> > > > > > >I am just using the modified force field parameters .
> > > > > > >But it is giving me syntax error.
> > > > > > >Can anyone guide me for the same.
> > > > > >
> > > > > > Your "leaprc.ff100" is not a leaprc-like file that can be sourced
> > > from
> > > > > > the command line in tleap. Instead, you need to use
> > loadAmberParams
> > > to
> > > > > > load in a file like this.
> > > > > >
> > > > > > The file format info at
> http://ambermd.org/FileFormats.php#frcmod
> > > > > > indicates that these files are fixed format, with entries in
> > > particular
> > > > > > columns. Your file is "free format", with just spaces between
> the
> > > > > > fields. I'm not sure whether loadAmberParams will work on that
> or
> > > not.
> > > > > > Note that the supporting information file you used has the data
> > > > > > carefully laid out in particular columns.
> > > > > >
> > > > > > ....dac
> > > > > >
> > > > > >
> > > > > > _______________________________________________
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> > > > > >
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Kellon A. A. Belfon, Graduate Student
> > > > Carlos Simmerling Laboratory
> > > > The Laufer Center for Physical and Quantitative Biology
> > > > The Department of Chemistry, Stony Brook University
> > > > Stony Brook, New York 11794
> > > > Phone: (347) 546-4237 <(347)+546+4237> Email:
> > kellon.belfon.stonybrook.
> > > > <kellon.belfon.stonybrook.edu>edu
> > > > _______________________________________________
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Received on Tue Mar 10 2020 - 11:00:02 PDT
