Also, you need to run some of the tutorials before you even try TGTMD
Plenty of problem with your input, such as you trying changing the
temperature (heating) and changing structure at the same time, using a
dt=0.2 instead of 0.002, and as far as I can tell, restraining your
structure with ntr AND attempting to change it at the same time.
Adrian
On 9/5/23 11:07 AM, Carlos Simmerling via AMBER wrote:
> [External Email]
>
> You have a typo, check the manual section for tgtmd. It should be
> tgtfitmask not tgtmdmask.
> Also make sure you have run stable md on the system using the same inputs
> (other than tgtmd). Here your ntb and ntp seem inconsistent.
> Your force constant for tgtmd is small. Keep that in mind if you aren't
> able to achieve the transition.
>
> On Tue, Sep 5, 2023, 10:35 AM Malcolm Lim via AMBER <amber.ambermd.org>
> wrote:
>
>> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Sep 05 2023 - 09:00:02 PDT
