[AMBER] Generate prmtop file using parmed.

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Thu, 7 Mar 2024 20:51:16 +0530

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 - 07:30:02 PST
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