AMBER Archive (2008)

Subject: Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params

From: ke dong (dongke83_at_gmail.com)
Date: Sat May 24 2008 - 09:46:19 CDT

I want to ask a question about the npopt thing,according to amber manual,when
NPOPT = 2 ,then RADIOPT should be 1,and this means using the radii
optimized by tan and luo,but there are no reference about that,can
anybody tell me
the exact name of that paper by tan and luo?
And i also want to know if the option NPOPT = 2 ,RADIOPT=1 cant be used when
dealing with protein and antechamber defined small molecule complex or not ?

because everytime i run MS=0,NPOPT=2,RADIOPT=1,it doesnt work,the result
shows missing surf data and stop at calculating the raw data?
thank you!

2008/5/23, Ray Luo <rayhuangluo_at_gmail.com>:
>
> Hi Marcin,
>
> Not sure this is answered or not ...
>
> The confusion originates from the different default settings in MMPBSA perl
> script and sander for nonpolar solvation free energies.
>
> If you turn on the option of NPOPT = 2, you can get desired output without
> setting any more parameters, i.e. the default values inside sander
> (CAVITY_SURFTEN = 0.04356 and CAVITY_OFFSET = -1.008) are for NPOPT = 2.
>
> All the best,
> Ray
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu