[AMBER] simulated annealing of DNA-ligand complex using NMR restrain

From: Anirban Ghosh via AMBER <amber.ambermd.org>
Date: Wed, 23 Aug 2023 18:35:34 +0000

Hello,

I was doing simulated annealing of DNA-ligand complex by using the following script.


&cntrl
    nmropt=1,
    ntpr=500,
    ntwx=500,
    nstlim=2000000,
    dt=0.0005,
    tempi=300.0,
    temp0=0.0,
    ig=-1,
    ntt=3,
    gamma_ln=5,
    ntc=2,
    ntf=2,
    ntb=0,
    tol=0.00001,
    cut=9999.0,
    igb=1,
    saltcon=0.050
 /
#
#
&wt type='TEMP0', istep1=0,istep2=400000, value1=300.0, value2=1000.0, /
&wt type='TEMP0', istep1=400001,istep2=1000000, value1=1000.0, value2=1000.0, /
&wt type='TEMP0', istep1=1000001,istep2=1800000, value1=1000.0, value2=0.0, /
&wt type='TEMP0', istep1=1800001,istep2=2000000, value1=0.0, value2=0.0, /

&wt type='REST', istep1=0,istep2=1000000,value1=0.1,value2=1.0, /
&wt type='REST', istep1=1000001,istep2=2000000,value1=1.0,value2=1.0, /

&wt type='END' /

LISTOUT=POUT
DISANG=complex_mod_R18m1.rst
END


I faced a problem with the geometry of methyl groups attached to one aromatic ring (quinolium ring) of ligand. Whether I put any NMR restrain related to the Methyl group or not I always getting a slight distorted geometry of the C-C bond connecting Methyl protons and aromatic carbon. I tried to play with the heating step but it did not solve the problem. Can you please suggest some modifications of the SA script above so that it will not distort?
Best Regards,
Anirban


Ph.D . Anirban Ghosh | CEITEC MU

Postdoctoral Fellow

Web: www.ceitec.eu<http://www.ceitec.eu/>

https://www.ceitec.eu/non-coding-genome-lukas-trantirek/rg109

Masaryk University

CEITEC – Central European Institute of Technology

Kamenice 5, 625 00 Brno, Czech Republic

Office no. A35/ASO22

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Received on Wed Aug 23 2023 - 12:00:01 PDT