Hi again,
Part of the internal pyRED procedure is linking the 2 together (that’s why
there’s a keyword section on inter-mcc), so one of the mol2 files in INTER
should be the complete nucleotide (if you used that keyword).
If you didn’t use it initially, I’d suggest rerunning based of their
tutorial or my own instructions.
-
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#19
-
https://emleddin.github.io/comp-chem-website/AMBERguide-PyRED-uploads.html
Sincerely,
Emmett Leddin
Pronouns: he/him
Chemistry PhD Candidate
> On Oct 16, 2020, at 08:13, Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
wrote:
>
> Thank you for the information;. I would try with the above procedure. But
*1LT E. Leddin, CAP*
(Cell) 708.522.7315
U.S. Air Force Auxiliary
gocivilairpatrol.com <
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On Fri, Oct 16, 2020 at 8:13 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:
> Thank you for the information;. I would try with the above procedure. But
> could you please tell how to join the dimethyl phosphate and the DNA base?
> Is it possible to do that directly in Xleap?
> Regards,
> Sruthi Sudhakar
>
>
> On Fri, Oct 16, 2020 at 5:35 PM Emmett Leddin <drtigger13.gmail.com>
> wrote:
>
> >
> >
> > Hi Sruthi,
> >
> > I’m not 100% sure about that leaprc.q4mddft script.
> >
> > The frcmod file with everything pyRED could find parameters for is in
> > Data-R.E.D.Server/Data-Default-Proj/frcmod.known . The parameters that
> are
> > missing (if any) are in (project folder/)
> > Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown . The INTER folder
> > should have a few mol2 files (since you used DMP, the one you want will
> > likely be named Mol-sm_m1-c1.mol2, but you should obviously confirm that
> it
> > looks right). If you used any 4-letter atom types, you likely have to
> > rename them to 3-letter types.
> >
> > If there were missing parameters, you can either search the literature or
> > use parmchk2 to attempt to find them.
> > parmchk2 -i Mol-sm_m1-c1.mol2 -f mol2 -o my_new_residue.frcmod
> > Then, copy the ones you need back into frcmod.known.
> >
> > From there, you can continue like you would with any non-standard,
> > wrangling it into the formats you want to use. Personally, I verify the
> > mol2 looks as expected in VMD, and then use VMD to write it as a PDB. At
> > this stage I do a quick test in xleap/tleap to make sure it doesn’t
> > complain about anything. [Note: there’s a tendency to have issues with
> > inter-residue connectivity for nucleic acids that usually won’t show up
> in
> > a one-off test. There’s a lot of good discussion in the archives on
> that.]
> >
> > Good luck!
> >
> > Sincerely,
> >
> > Emmett Leddin
> >
> > Pronouns: he/him
> > Chemistry PhD Candidate
> >
> > >> On Oct 16, 2020, at 04:50, Sruthi Sudhakar <
> > sruthisudhakarraji.gmail.com> wrote:
> > > Dear all,
> > > I have generated forcefield parameters for a modified DNA base using
> RED
> > > server. Following the tutorial, I made 2 pdb files, one of
> > > dimethylphosphate and second of the modified DNA base. I have obtained
> > the
> > > output data and now confused regarding how to proceed forward. I have
> the
> > > leaprc.q4mddft script. Could someone explain the procedure of including
> > the
> > > R.E.D server parameters into xleap?Do we need to modify the
> > leaprc.q4mddft
> > > file? Also how could I combine my molecules and place them inside a
> > duplex?
> > > Is there any tutorial available for this.?
> > > Thanking in advance.
> > > Regards,
> > > Sruthi Sudhakar
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 16 2020 - 10:30:03 PDT
