Hi Ning,
My two cents. You can refer to this paper for restraint set-up, which might help with the potential sampling issue, if there’s any.
https://pubs.acs.org/doi/abs/10.1021/jp0217839. And I suggest you to use the AMBER 20 released earlier this year as well, since there was multiple updates from previous version:
https://chemrxiv.org/engage/chemrxiv/article-details/60c73cc94c891981e9ad1af3
Best,
Lin
> On Sep 28, 2021, at 1:39 AM, neildancer.sina.com wrote:
>
> Hi, Amber experts,
> Sorry to bother you. I was using pmemd tool of the cuda version to calculate the ABFE(absolutely binding free energy) of HIV protease and ritonavir drug (This PDB ID number of the complex structure is 1HXW), with different product running time, such as 1ns and 10ns. And, the remaining parameters of ABFE calculate were same at both. About the necessary restraint option, the C12,C13 atoms were choosen to define the relative position with wt_restraint = 10, and wt_mask option. The detail information about restraint, please refer to the attached file. However, due to the different product time, I got the totally different ABFE results. When it run 1ns, the ABFE was -20 kcal/mol. But, when it run 10ns the ABFE was nearly zero. I don't know which cause lead this. Please point my errors. The input file were also attached with this email.
>
> Best regards,
>
> --------------------------------
>
> Ning Wang <PhD>
> National Laboratory of Biomacromolecules
> Institute of Biophysics, Chinese Academy of Sciences
>
>
> My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.
> ORCID:https://urldefense.com/v3/__https://orcid.org/0000-0002-5019-2747__;!!HXCxUKc!kAzQD88SM1DobubQaMWHiez9-bcne8O1jl17b36VnerrgHQuPIFO5NbLpTSniisGVcdfH1xV$
>
> <C12_C13_RTV.png><ti.in.template>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!HXCxUKc!kAzQD88SM1DobubQaMWHiez9-bcne8O1jl17b36VnerrgHQuPIFO5NbLpTSniisGVfZNGQ2O$
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 28 2021 - 13:00:03 PDT
