Hi all,
Does Amber 11 contain OPLS-AA force-field?
Can i simulate polarisable ions £¨with polarisable water£©£¿
Which force-field is suitable for run just water with ions?
Thanks
At 2011-04-03 23:47:59£¬"Sangita Kachhap" <sangita.imtech.res.in> wrote:
>
>Hello all
>
>I am study water mediated protein-DNA interaction.
>What I have did remove all crystalized water and add TIP3P water 6 angatrsom
>from protein-DNA surface.
>
>Minimize first water + ions then finally whole system
>
>Heat the system from 0 to 300K at NVT for 200ps using positional restraint on
>protein-DNA
>
>Decrease positional restraint for 200ps at NVT
>
>Equilibrate the system at NPT for 600ps
>
>Production MD for 6ns
>
>I have generated prmtop for system have 10 water molecules
>When I visualize trajectory using above prmtop water moleclues are so far from
>mask residue
>
>Though when I check number of water moleclues around mask residue using
>watershell command lower range 3 angostrom
>and upper range 5 angostrom, water molecules are present at both range.
>
>I am not getting why processed trajectry not showing water molecule close to
>mask residue.
>
>
>
>With regards
>
>Sangita Kachhap
>JRF
>BIC,IMTECH
>CHANDIGARH
>
>
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Received on Mon Apr 04 2011 - 03:30:04 PDT
