On Mon, Feb 20, 2017 at 1:36 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Dear Dr. Case,
>
> Thank you for your answer about the FFs and DNA/RNA complexes. The bottom
> line is, I gather,
> that I should use both RNA and DNA parameters and that, in principle they
> can be employed with GB-neck2
> after proper PBradii are set.
>
> I apologize for my delayed response. I did not have full access to all the
> data over the weekend.
> I retested leap sessions in Amber 14 environment on two machines (separate
> campuses and administrators),
> and they both yielded identical PDB and PRMTOP output after leaprc.ff14SB
> & leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1
> were sourced (DNA chains have phosphate groups with P, O1P and O2P atom
> names and are capped by H5T & H3T, while
> RNA chains use PDB 3.x standard).
>
> One of our systems has Amber 16 installed and leap returns uniform atom
> names for DNA and RNA (P, OP1, OP2 and HO5'
> and HO3' respectively) after leaprc.RNA.OL3 and leaprc.DNA.OL15 are
> sourced.
> Unfortunately I ran into
> some criptic failure after the" addions mol Na+ 0" command
hi, what is the failure?
> and could not produce PRMTOP file for comparison with
> the previously created Amber 14 equivalent.
PRMTOP files between two versions are expected to be different. You should
check the energies.
(Dan Roe said a bit in topic:
[AMBER] Differences using leaprc.ff14SB from AmberTools15 and
oldff/leaprc.ff14SB from AmberTools16)
Hai
> (I will have to resolve this issue with our scientific apps administrators,
> since that was never a problem in the past.)
>
> If anybody can offer comments or warnings about RNA/DNA simulations, I
> will appreciate it very much.
>
> Best regards, Voytek Kasprzak
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
>
> ________________________________________
> From: David Case [david.case.rutgers.edu]
> Sent: Saturday, February 18, 2017 3:33 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure
>
> On Fri, Feb 17, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> >
> > I am trying to run an Amber 14 MD simulation (explicit solvent, PME
> > and/or implicit solvent GB-neck2) of a hybrid nucleic acids structure
> > of 4 chains (2 DNA, 2 RNA) forming two DNA/RNA helices and one all-DNA
> > helix.
> >
> > I built two sets of parameter files (incl. water box and ions), one
> > based on leaprc.ff14SB ONLY (plus frcmod.ionsjc_tip3p) and the other
> > with leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1.
> >
> > I can immediately see that the DNA atoms in an output PDB files have
> > different names for the dual ff LEaP, and there are numerous differences
> > in the topology parameters files.
>
> Can you provide an example of the name differences? We re-worked the
> nomenclature for force fields in 2016 (for AmberTools16), and it's a little
> hard to go back to figure out how things used to be. I had thought that
> all our files had used IUPAC/PDB names for nucleic acids for some time.
>
> >
> > 1. Which is the correct (or better) way of preparing a DNA/RNA
> > simulation, and what is the meaning of a warning in the Amber 14 manual
> > (section 3.2.2) regarding the chi (chiOL4) modifications and shared
> > naming conventions for RNA and DNA.
>
> This, I think, has to do with atom *types*, not atom names; but atom types
> don't appear in PDB files.
>
> I'll leave it up to others to comment on any potential problems with
> DNA/RNA
> duplexes.
>
> >
> > 2. Can the same LEaP approach be applied to implicit solvent simulations
> > (GB-HCT igb=1 & mbondi and/or Gb-neck2 ibg=8 & mbondi3)?
>
> You need to either specify the PBRadii to be used at the time LEAP is run,
> or
> use ParmEd to change the radii after the fact. The igb choice is made at
> the
> time sander or parmed is run.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2017 - 12:00:04 PST
