Minimization is less important overall than it seems at first. I'm not
practicing but suspect ambpdb is still fine, unless other methods might
provide CONECT records if ambpdb doesn't, if it matters.
I'd be looking forward to viewing the trajectories in VMD, like this, as
of VMD 1.9.2:
https://ambermd.org/tutorials/basic/tutorial2/section6.htm
Bill
On 12/15/20 11:29 PM, Jisha B wrote:
> ambpdb did work and I got a pdb file from the restart file of minimization.
> I just want to know the usual practice after minimizing some newly modelled
> structures.
>
> On Wed, 16 Dec 2020 at 12:56, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I bet you could try it and report back faster than I could look it up,
>> fwiw. :-)
>>
>> Bill
>>
>>
>> On 12/15/20 11:23 PM, Jisha B wrote:
>>> I have modelled a protein in a few places and so minimized the structure
>> in
>>> AMBER before using it to form a complex with a ligand. So after a
>>> minimization of 10000 steps in AMBER18, I need the pdb file of the
>> protein.
>>> So is it enough to use the ambpdb or is there any other method for the
>> same?
>> --
>> Phobrain.com
>>
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>>
>
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Phobrain.com
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Received on Wed Dec 16 2020 - 00:00:02 PST
