Dear David,
Thanks for the response!
Yes, the perturbation file and everything is created ok (I have run the
same thing using gibbs FEP and then it works i.e. free energies are
calculated).
Now I just want to try it out with TI in sander and TI in gibbs.
This is the gibbs FEP input that I use:
&cntrl
dt=0.002,
ntx=7,
ntpr=100,
temp0=300,
ntt=5,
tautp=2.0,
ntb=2,
ntp=1,
ntc=2,
ntf=2,
nsnb=5,
scee=1.2,
scnb=2.0,
nstlim=2000,
nstmeq=1000,
nstmul=1000,
intprt=1,
nrun = 21,
almda = 1.0,
almdel = 0.05,
isldyn = -3,
&end
And I would want to have a corresponding TI input (for gibbs and one for
sander) for comparison.
Thanks in advance!
/Annette
david.evans.ulsop.ac.uk wrote:
>Hi,
>
>Have you set up your prmtop file with the correct information for the
>perturbation? I.e. in leap input commands like (randomly pulled from
>one of my systems, read the manual for yours)
>
>set complex.90.C2 pert true
>set complex.90.C2 pertName N1
>set complex.90.C2 pertType nd
>set complex.90.C2 pertCharge -0.0693
>.....
>saveAmberParmPert complex prmtop prmcrd
>
>The first "pert true" command is missing (I think) from the Amber8
>manual, but seems to be necessary.
>
>Dave Evans
>London School of Pharmacy
>
>
>---- Message from Annette Ho"glund
><hoeglund.informatik.uni-tuebingen.de> at 2004-11-02 11:44:03 ------
>
>
>>Dear All,
>>
>>I have been experiencing the same thing (zeros everywhere and no free
>>energy is collected) when trying to perform TI using sander. I
>>
>>
>perform
>
>
>>minimization and equilibration (as I would do for a simulation)
>>
>>
>before
>
>
>>the TI step.
>>Could someone help and perhaps post an input for sander TI (and
>>
>>
>perhaps
>
>
>>also the min and equil input before that) applicable to a protein?
>>
>>Regards,
>>Annette
>>
>>
>>Xiao He wrote:
>>
>>
>>
>>>Dear Amber users,
>>> I want to use thermodynamic free energy calculations,
>>>
>>>I read the manual and try a system like this
>>>
>>> nstlim=1000,ntpr=100
>>> icfe=1,
>>> clambda=0.5,
>>> klambda=4,
>>> ntb=0,
>>> temp0 = 300.0, tautp = 1.0,
>>> ntf = 2, ntc = 2,
>>> dt = 0.002,
>>> ntave = 25,
>>>
>>>But it seems it does not calculate the free energy.
>>>
>>>
>>>
>>>
>>>
>>>
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Received on Tue Nov 02 2004 - 12:53:00 PST
