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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Received on Fri Oct 16 2020 - 05:30:03 PDT
