No, I used eps 1.0. The input for anal is as follows:
test of anal energies
1 0 0 0 0 1
0 0.0 0.0 0.0 0.0
1 0 0 0 0 0
99.0 2.0 1.2 1.0
1 10.0 10.0 10.0 10.0 10.0 10.0 20.0 10.0 10.0
ENERGY
First alpha helix 1
RES 4 11
....
and input for min is as follows:
gb minimization
&cntrl
imin=1, maxcyc=1000,
cut=99.0, igb=2, saltcon=0.2, gbsa=1,
ntpr=100, ntwr=100, ntt=0,
ntb=0,
&end
Piotr
On Fri, 27 Jan 2006, David A. Case wrote:
> Date: Fri, 27 Jan 2006 13:33:57 -0800
> From: David A. Case <case.scripps.edu>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: anal vs sander
>
> On Fri, Jan 27, 2006, Piotr Cieplak wrote:
>>
>> I minimized a protein using infinite cutoff , and igb=2 (gb/sa +
>> saltcon=0.2) and then the last structure I reanalized using ANAL program..
>> For this given particular structure I got all energy components the same
>> besides 1-4 elstat and elstat , which in the case of GB/SA were 4 times
>> larger values.
>>
>> I used in both cases the same cutoff. And I know that anal is decomissioned...
>
> Is it possible that you set a dielectric of 4 in the ANAL input?
> (This would be the last number on line 5 of the anal input)
>
> ...dac
>
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Received on Sat Jan 28 2006 - 06:10:07 PST
