Thanks Francois! I will check this.
*----------------------------------------*
*Prabir Khatua, PhD*
*Assistant Professor, Department of Chemistry*
*GITAM School of Science *
*GITAM (Deemed to be University)*
*Bengaluru-562163**, India*
*Website: https://prabir07chem.wixsite.com/computational-biophy
<
https://prabir07chem.wixsite.com/computational-biophy>*
--------------------------------------
On Thu, Aug 8, 2024 at 7:50 PM FyD via AMBER <amber.ambermd.org> wrote:
> Dear Prabir,
>
> You could use REDServer Development @:
> https://upjv.q4md-forcefieldtools.org/REDServer-Development/
>
> See tutorial .:
> https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
> https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#SpltV
> https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#IV1
> https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#V2
> https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo5.pdf
>
> I hope this helps
> Best Francois
>
>
> > As I mentioned in my earlier email that I am going to follow the
> procedure
> > suggested by Carlos to preserve OL15 description as much as possible. I
> am
> > still seeking a suggestion regarding the charge parameterization. To get
> > the charge parameters, I am doing an optimization using gaussian 16 with
> > B3LYP/6-31G* followed by RESP charge calculation at HF/6-31G* level. The
> > charge distribution that I got is significantly different from the
> > unprotonated cytosine of the original OL15 parameter for all the atoms
> > including sugar and phosphate. Please note that I am doing the
> optimization
> > and the RESP charge calculation on the entire protonated cytosine
> including
> > sugar ring and phosphate. While such charge redistribution is expected
> due
> > to the protonation of cytosine N3, I am wondering if a better approach
> > might be to optimize and calculate the charge of the base alone, so that
> > there is no need to change the charge distribution in the sugar or
> > phosphate. This would help in obtaining the new charge distribution,
> > preserving the OL15 description to the maximum extent. Please comment on
> > this.
> >
> > I appreciate any help/suggestion.
> >
> >
> > On Thu, Aug 8, 2024 at 8:59 AM Prabir Khatua <pkhatua.gitam.edu> wrote:
> >
> >> Thanks Carlos for the reply! Loading the frcmod file before the mol2
> file
> >> worked for me.
> >>
> >> In fact, I wanted to follow the complex procedure you mentioned that is
> >> taking OL15 force field parameters as much as possible and then using
> the
> >> gaff generated parameter for the added part.
> >>
> >> Thanks once again for the suggestion and help!
> >> Prabir
> >>
> >> On Wed, 7 Aug 2024 at 7:13 PM Carlos Simmerling <
> >> carlos.simmerling.gmail.com> wrote:
> >>
> >>> others here may have more detailed info for you, but the frcmod file
> you
> >>> shared does indeed have the o-p3-os params, you might want to try
> loading
> >>> those parameters before you load the mol2, not after.
> >>> also the log file gets appended every time you run it, so it can be
> more
> >>> helpful if you remove the log file before re-running leap so that it
> >>> contains only the most recent attempt. otherwise it contains the
> history of
> >>> previous errors even if they were fixed later and it is more difficult
> to
> >>> follow.
> >>>
> >>> some other suggestions: loading multiple leaprc files can get
> confusing.
> >>> for example, loading both gaff and gaff2 should not be needed, you
> should
> >>> choose 1 and use that. also it looks like you have no standard DNA
> here so
> >>> loading the OL15 learprc is not needed.
> >>>
> >>> finally, keep in mind that using gaff/gaff2 for your DNA will mean that
> >>> the entire monomer is described by gaff, and it will not have any of
> the
> >>> DNA-specific adjustments applied to that monomer (backbone dihedrals,
> sugar
> >>> puckers and so on). This means it may behave differently from standard
> >>> cytosine just because of the parameter differences and not only
> because of
> >>> the protonation change. To be more clear, a standard cytosine using
> gaff
> >>> and using OL15 will not necessarily behave the same, so you need to be
> >>> careful in how you interpret the results of the protonation. A better
> (but
> >>> more complex) approach would be to use the OL15 parameters as much as
> >>> possible, and then use gaff only for the part of the monomer that
> differs
> >>> from the standard base. This would preserve the OL15 description as
> much as
> >>> possible. This does require some force field expertise, and you may get
> >>> more specific advice from experts here in DNA force fields.
> >>>
> >>> On Wed, Aug 7, 2024 at 3:26 AM Prabir Khatua via AMBER <
> amber.ambermd.org>
> >>> wrote:
> >>>
> >>>> Dear Amber users,
> >>>>
> >>>> I am getting the following error while trying to generate the force
> field
> >>>> for a protonated cytosine (not as 5' or 3' or neutral one) using the
> >>>> OL15
> >>>> force field in Amber 24.
> >>>>
> >>>> /apps/scratch/compile/amber24/bin/teLeap: Error!
> >>>> Could not find angle parameter for atom types: o - p3 - os
> >>>> for atom O1 at position -3.028000, -2.260000, 1.553000,
> >>>> atom P1 at position -2.521000, -1.721000, 0.281000,
> >>>> and atom O3 at position -3.395000, -0.527000, -0.304000.
> >>>>
> >>>> /apps/scratch/compile/amber24/bin/teLeap: Error!
> >>>> Could not find angle parameter for atom types: o - p3 - os
> >>>> for atom O2 at position -1.455000, -2.224000, -0.617000,
> >>>> atom P1 at position -2.521000, -1.721000, 0.281000,
> >>>> and atom O3 at position -3.395000, -0.527000, -0.304000.
> >>>>
> >>>> It seems like it's unable to find the above mentioned parameter.
> >>>> However, I
> >>>> do not know which force field I should source. For your information,
> I am
> >>>> attaching the entire log file, input leap file, mol2, and frcmod
> files if
> >>>> needed. Please help me to fix this issue.
>
>
>
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Received on Thu Aug 08 2024 - 23:30:02 PDT
