Dear Prof. Case,
As usually in double decoupling calculation, in V1 state, the ligand still remains, but just not interacted with protein( it is in gas state and usually contraint in origin position). So I still need the ligand in top and crd file. Dr. Donald Hamelberg suggested me to make a frcmod file and modify the vdw parameter to 0.0, but this will also did not calculate the ligand intramolecular interaction. I am wondering is there other way for just turn off the vdw interaction?
Thanks !
Bing
case <case.biomaps.rutgers.edu> ÔÚ Fri, 30 Dec 2011 20:19:35 дµÀ£º
>On Sat, Dec 31, 2011, Bing Xiong wrote:
>>
>> By reading the manual (amber 10), the softcore part stated that we
>> can turn off the charge with crgmask. Can we turn off the vdw interaction of
>> ligand with protein as commonly used in double decouping
>> calculations? how to do this in amber? such as how to prepare the V1
>> state(V0 is the vdw interaction on, charge=0.0 )? is there any parameter
>> like crgmask for turn off the VDW interaction?
>
>If I understand your question correctly, the usual way to prepare a "V1"
>state where there is no coupling between the ligand and the environment is
>simply to leave the ligand out when making the prmtop file. The TI
>implementation in sander does not require the same number of atoms in the two
>end states.
>
>Please see tutorial A9 for a worked-out example.
>
>...dac
>
>
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Received on Sun Jan 01 2012 - 23:00:03 PST
