Hai, Amber Users,
Thank you for your reply on the RNA/Ligand simulations with the GB neck2 protocol.
I found a lot of small differences and some striking ones for the S and C atoms in a benzothiopene module of
a ligand's (Arzoxifene-HCl, constant input file geometry) partial charges computed by an antechamber
command line call and a call to antechamber from Chimera (1.11.2) .
The ligand is positively charged (+1), and the (Amber 14) antechamber call I used was as follows:
> antechamber -i LIG.pdb -fi pdb -o LIG-A14ante-bcc.mol2 -fi mol2 -nc 1 -m 2 -s 2
The total charge and multiplicity of 2 deal with the odd number of electrons (-j 4 is the default atom and full bond type)
Chimera GUI, on the other hand, issues the following command:
> antechamber -ek qm_theory='AM1', -i LIG.mol2 -fi mol2 -o LIG-ante.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
Thus the multiplicity of 1 is assumed (default) and -j 5 - atom and part bond type.
Input of MOL2 type must be internally converted, since I read in a PDB file.
Which is the correct way to go, or what are the compromises these two calls make?
Best regards, Voytek Kasprzak
Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Hai Nguyen [nhai.qn.gmail.com]
Sent: Tuesday, October 24, 2017 10:31 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible
On Tue, Oct 24, 2017 at 1:57 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
wojciech.kasprzak.nih.gov> wrote:
> Dear Amber Users,
>
> Over the last year I became comfortable with the GB neck2 results for
> RNA-only simulations,
> even though we still run explicit solvent simulations in parallel. Now, I
> have tried for the first
> time an RNA fragment with a small molecule for which the partial charges
> and the parameters
> were derived via Amber 14 antechamber and parmcheck (PDB to MOL2, then
> FRCMOD and PREP files).
> LEAP accepted these files together leaprc.gaff, leaprc.ff14SB and with
> "set default PBradii mbond3"
> for in igb=8 / mbondi3 run. PMEMD.cuda runs well, but we see a lot more
> RNA motion with one of the
> tested ligands than we have seen for the RNA alone. This is either very
> interesting or seriously off.
>
> Do you have any recommendations for or against GB neck2 runs of RNA with
> ligands? The Sustiva-RT
> tutorial (Amber tutorial 4B) does not rely on explicit solvent, but the
> receptor there is a protein...
>
>
> Hoping to hear from anybody who tested the above combination.
> Best regards, Voytek Kasprzak
>
hi, sounds like you're very first person trying this.
We only tested the simulation with the binding of a ligand to minor groove
of the DNA duplex (saw the rebinding if taking the ligand out of the pocket
from x-ray structure; but this won't tell anything)
Hai
>
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 25 2017 - 14:30:01 PDT
