[AMBER] Amber problem looking for help

From: leveen via AMBER <amber.ambermd.org>
Date: Fri, 4 Aug 2023 09:54:30 +0800

Dear Amber community,
&nbsp; Referring to tutorial Amber tutorial - Protein Ligand binding free energies (ambermd.org), I'm trying to run the QM/MM simulation to&nbsp; collect potential energy differences for FEP calculations.&nbsp;The version I am using is Amber22. The simulation process is calculated using Sander.
&nbsp; When I generated an input file using the new version of the mbar method in the Amber22 manual, an error was reported('error in reading namelist cntrl').&nbsp;
Here is the input file:
NPT simulation
&nbsp;&amp;cntrl
&nbsp; irest=0,ntx=1,
&nbsp; nstlim=50000,dt=0.002,
&nbsp; temp0=300.0,ntt=3,gamma_ln=2.0,
&nbsp; ntc=2,ntf=1,
&nbsp; cut=8.0,
&nbsp; ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
&nbsp; icfe=1,clambda = 0.5,
&nbsp; ifmbar=1,
&nbsp; mbar_states = 15,
&nbsp; mbar_lambda = 0.00, 0.05, 0.10, 0.15, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.85, 0.90, 0.95, 1.0,
&nbsp; ifsc=1,scmask=":PHN.O1,H6",
&nbsp; ifqnt = 1,
&nbsp;/
&nbsp; &amp;qmmm
&nbsp; qmmask=':PHN.1-13',
&nbsp; qmcharge=0,
&nbsp; qm_theory='DFTB3',
&nbsp;/

&nbsp; And my terminal's command is&nbsp; ' mpirun&nbsp; -np 2&nbsp; sander.MPI -ng 2 -groupfile group_prod_l ' .
&nbsp; When I generate an input file using the old version of Amber method, it can be run. The input file is as follows:
NPT simulation
&nbsp;&amp;cntrl
&nbsp; irest=0,ntx=1,
&nbsp; nstlim=500000,dt=0.001,
&nbsp; temp0=300.0,ntt=3,gamma_ln=2.0,
&nbsp; ntc=2,ntf=1,
&nbsp; cut=8.0,
&nbsp; ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
&nbsp; icfe=1,clambda = 0.5,
&nbsp; ifmbar=1, bar_intervall=1000,bar_l_min=0.005,bar_l_max=0.995,bar_l_incr=0.1,
&nbsp; ifsc=1,scmask=":BNZ.H6",
&nbsp; ifqnt = 1,
&nbsp;/
&nbsp; &amp;qmmm
&nbsp; qmmask=':BNZ.1-12',
&nbsp; qmcharge=0,
&nbsp; qm_theory='DFTB3',
&nbsp;/


&nbsp; However, in the old version of Amber method,&nbsp;it is not allowed for bar_l_min&gt;0.995 or bar_l_max<0.005, which makes it impossible for me to set the lambda=0,1.
&nbsp; How should I do£¿
&nbsp; Best wishes!
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Leveen




&nbsp;

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Received on Thu Aug 03 2023 - 19:00:02 PDT
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