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
http://jswails.wikidot.com/parmed. 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 - 02:00:02 PDT
