[AMBER] ff14SBonlysc + OPC3

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Mon, 29 Jun 2020 15:40:11 +0300

Dear community,

I am a little confused on the usage of OPC3 water model. I am trying to update my tleap files to use ff14SBonlysc + OPC3BOX water forcefields for my runs, but I am not sure how to source everything correctly. This is the leap input I wrote, which works, but if I don’t include source leaprc.water.tip3p, it doesn’t. As shown below I am loading the tip3p model, with a OPC3 box, is that correct?

I tried with a leaprc.water.opc3 command but it gives an error. Also If I add the loadAmberParams frcmod.opc3 to the input file, again it works, but I am not sure I am doing the right thing.

Can anybody please enlighten me?
I read the manual, but it is really a little tricky.


==== tleap input ===

source leaprc.protein.ff14SBonlysc
source leaprc.water.tip3p

loadAmberParams frcmod.ionsjc_tip3p
set default PBradii mbondi3

MOL1 = loadpdb 6HD5.TU.scwrl4.molprobity.clean.pdb

savepdb MOL1 com.nata.YEAST.6HD5.20A.opc3.dry.pdb
saveamberparm MOL1 com.nata.YEAST.6HD5.20A.opc3.dry.prmtop com.nata.YEAST.6HD5.20A.opc3.dry.rst7

solvateoct MOL1 OPC3BOX 20

addions MOL1 Na+ 0
addions MOL1 Cl- 0

savepdb MOL1 com.nata.YEAST.6HD5.20A.solv.pdb
saveamberparm MOL1 com.nata.YEAST.6HD5.20A.solv.prmtop com.nata.YEAST.6HD5.20A.solv.rst7




Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701

AMBER mailing list
Received on Mon Jun 29 2020 - 06:00:06 PDT
Custom Search