Hi Dulal,
See an archived response from Dr. Jason Swails to a similar post: http://archive.ambermd.org/201708/0286.html
If my understanding is correct, this function does not remove any (ghost or real) hydrogens, but alters the charge of the titratable residues in CpHMD simulations. It is not supposed to change the residue names or topologies - GL4 will stay as GL4, HIP will stay as HIP – so that that the output prmtop is still useful for CpHMD simulations.
Bests,
Amy
From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Thursday, March 7, 2024 at 10:22 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Generate prmtop file using parmed.
Dear Experts,
I am trying to generate two prmtop files. 1) Histidine 64 in state 1
(deprotonated state) and 2) Histidine 64 in state 2 (deprotonated state)
from a prmtop file (named as amber18.prmtop). I generate this
(amber18.prmtop) prmtop file during constant pH md simulation. In the
ambercpin.prmtop all His are in HIP (doubly protonated) state. Now I am
trying to generate two prmtop files using parmed.
parmed -i script.in -p amber18.prmtop -c nvtequi.ncrst.
In script.in file contains
changeProtState :62 1
parmout amber18_1.prmtop nvt1.ncrst
But in amber18_1.prmtop also in HIS in HIP state.
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Thu Mar 07 2024 - 13:00:02 PST
