Re: [AMBER] Hamiltonian REMD simulation

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 13 Mar 2024 15:55:23 +0000

Hi Dulal,

It might be that the radii were somehow unset in the new prmtop. If you’re not sure, view 'modified_topology_lambda_1.0.prmtop' as a text file and check the sections (near the end) that begin with %FLAG RADIUS_SET and %FLAG RADII. FLAG RADIUS_SET gives you the title of the radii set like `H(N)-modified Bondi radii (mbondi2)`, and RADII gives the numbers. Compare them to your original prmtop file.

You can set the radii by the changeRadii function in ParmEd, or just copy and overwrite the whole sections if you didn't want to change the radii and the ordering of the atoms :> 


--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Wednesday, March 13, 2024 at 4:58 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Hamiltonian REMD simulation
Dear Experts,
I run constant ph MD as well as constant pH remd. Though both protonation
states (0 and 1) are not sampled. The experimental pka of side chain TYR 5
is 7.1.  At pH higher than 9.0 it remains 100 percent in protonated state.
I followed the tutorial https://urldefense.com/v3/__http://jswails.wikidot.com/parmed__;!!KGKeukY!x996eiz5U1k5zWuaTT8v4F-6LjBR4nbFB1Ni1SYqhUDecqNDzrKhbUT2-O3rxgDdc7dH1ftY2VbiJHq3fEl7yxIKQY8$<https://urldefense.com/v3/__http:/jswails.wikidot.com/parmed__;!!KGKeukY!x996eiz5U1k5zWuaTT8v4F-6LjBR4nbFB1Ni1SYqhUDecqNDzrKhbUT2-O3rxgDdc7dH1ftY2VbiJHq3fEl7yxIKQY8$> . I am trying to
generate different prmtop files for this purpose. I generated 6 prmtop
files from an initial pemtop file (amber18.prmtop) with varying charge of
the HH atom of TYR 5 residue in my protein.
I created the following prmtop files with varying charges of the HH atom of
TYR 5. I also calculate charge of the HH atom using cpptraj command (charge
:5.HH)
*amber18.prmtop (initial prmtop) (Sum of charges in mask [:5.HH](1) is
0.3992)*
*modified_topology_lambda_0.0.prmtop  (Sum of charges in mask [:5.HH](1) is
0.3992)modified_topology_lambda_0.2.prmtop  (Sum of charges in mask
[:5.HH](1) is 0.31936)modified_topology_lambda_0.4.prmtop  (Sum of charges
in mask [:5.HH](1) is 0.191616)modified_topology_lambda_0.6.prmtop (Sum of
charges in mask [:5.HH](1) is 0.0766464)modified_topology_lambda_0.8.prmtop
(Sum of charges in mask [:5.HH](1) is
0.0153293)modified_topology_lambda_1.0.prmtop (Sum of charges in mask
[:5.HH](1) is 0)*
*I set a lambda value [0.0, 0.2, 0.4,0.6,0.8,1.0] for generating different
prmtop files.*
*But when I load the original prmtop file (amber18.prmtop) in cpptraj it
shows the following message.*
Reading 'amber18.prmtop' as Amber Topology
*Radius Set: H(N)-modified Bondi radii (mbondi2)*
Loading previous history from log 'cpptraj.log'
But when I load the modified topology file it shows radius set 0 for all
modified files.
Reading 'modified_topology_lambda_1.0.prmtop' as Amber Topology
Radius Set: 0
*Is this correct or not?*
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Mar 13 2024 - 09:00:03 PDT
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