Now again I tried with Amber tools 1.4 , pbsa
using my input script for default values mostly and though this runs to give
my output, Here I have attached my .out file ,please see if you can access
it.
I would like to know about
PB Info in pb_read(): npopt has been overwritten with inp
How does this rectify to get the input for atom radius. Can you clarify me
to get the exact solvent accessible surface area for my molecule.
As per manual I used sprob = 1.6 , which was the default value.Which ither
parameters I should take into consideration in my input , if I have some
atoms like Iron.
Thanks for any suggestion
Kirtana
On Mon, Sep 12, 2011 at 12:05 PM, kirtana S <skirtana4.gmail.com> wrote:
> Thanks for your reply
> I am using amber10. bin/pbsa for my calculations
>
>
>
>
> On Mon, Sep 12, 2011 at 12:00 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Kirtana,
>>
>> I think your reading is correct. Which release are you using?
>>
>> All the best,
>> Ray
>>
>> On Mon, Sep 12, 2011 at 8:56 AM, kirtana S <skirtana4.gmail.com> wrote:
>> > I am using pbsa to calculate solvent accessible surface area ,
>> >
>> > &cntrl
>> > imin =5,
>> > igb=10,
>> > gbsa=2,
>> > surften=1,
>> >
>> > &pb
>> > epsout=80,
>> > &end
>> >
>> > It sends me an error as
>> > PB Bomb in pb_aaradii(): no radius assigned for atom 681 1fe
>> >
>> > I have a iron atom in my input file,in the manual it says if I set
>> radiopt=0
>> > this should use the radii from
>> > prmtop file for both PB calculation and for NP calculation. Here I get
>> >
>> > PB Bomb in pb_read(): use of radii other than vdw sigma for
>> > np solvation dispersion/cavity is not supported!
>> >
>> > How can I set up the radii and calculate the solvent accessible surface
>> area
>> > if I use radiopt =1
>> >
>> > I appreciate your suggestion.
>> >
>> > Thanks
>> > Kirtana
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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>>
>
>
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Received on Mon Sep 12 2011 - 12:00:03 PDT
