Have you tried skipping the SA and doing either minimization or md? It may
be in your ligand parameters. It is also possible that this old gb model is
not ideal for that ligand.
On Wed, Aug 23, 2023, 2:36 PM Anirban Ghosh via AMBER <amber.ambermd.org>
wrote:
> 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 - 12:30:03 PDT
