Dear Sir/Ma'am,
I am new to AMBER and am trying to use AMBER22 for a Targeted MD (TMD) simulation, with my objective being trying to simulate the transition between 2 conformational states of a specific protein. I am starting with the .pdb files of both conformational states.
I've read through the manual and have prepared the pdb files via tleap, and have used the following script to prepare both structures in tleap (e.g. for state 'c' to state 'm'):
#tleap_c.in
source leaprc.protein.ff19SB
source leaprc.water.opc
#loadamberparams frcmod.ions1lm_126_hfe_opc
c=loadpdb cState.amber.pdb
SaveAmberParm c c_gas.prmtop c_gas.inpcrd
addIons c Na+ 13
solvateOct c OPCBOX 10.0
addIonsRand c Na+ 35 Cl- 35
SaveAmberParm c c_ion.prmtop c_ion.inpcrd
Using the prmtop and inpcrd files, I've attempted to run the TMD on sander via the following command:
sander -O -i tmd.in -o tmd.out -p c_ion.prmtop -c c_ion.inpcrd -r tmd.ncrst -ref m_ion.inpcrd -x tmd.nc
where tmd.in contains the following:
TMD
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=10000,
dt=0.2,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntpr=100,
ntwx=100,
cut=8.0,
ntb=2,
ntp=0,
ntt=3,
gamma_ln=2.0,
itgtmd=1,
tgtmdfrc=0.005,
ntr=1,
restraint_wt=10.0,
restraintmask=":1-279",
tmdmask=":1-279",
tgtrmsmask=":1-279"
/
&wt type='TGTRMSD', istep1=0.0, istep2=10000, value1=3.663, value2=0.0
/
&wt type='END'
/
However, I've run into an error: "error in reading namelist cntrl", which indicates that perhaps the syntax of the .in file is amiss, though I'm uncertain of what is wrong. I just have 2 questions for the above:
1. Could I check if there is anything wrong with the .in file that is causing this issue? Or perhaps something wrong with the parameters in the command line and/or in the preparation of the necessary prmtop/inpcrd files?
2. Could I also ask if the parameters in the .in file are appropriate for the purpose of this TMD run? Or am I missing out other factors that should be considered when executing such a simulation of this nature?
Thank you very much and looking forward to learning more about AMBER!
Best wishes,
Malcolm
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Received on Tue Sep 05 2023 - 08:00:01 PDT
