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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
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 Sun Mar 08 2020 - 15:30:01 PDT
