Hi Sunita,
“desc” command is not in the bin folder, it is a command inside LEaP. You can check the Page 224 of the AMBER 2018 manual: http://ambermd.org/doc12/Amber18.pdf <http://ambermd.org/doc12/Amber18.pdf>.
Pengfei
> On Mar 2, 2019, at 2:26 AM, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> My case is simple. I am trying to simulate Ca2+ coordinated to protein.
> Thank you.
>
> On Sat, Mar 2, 2019 at 1:13 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Note that if you're trying to simulate a covalently bound calcium, you
>> may want to generate parameters using MCPB.py since it's not clear the
>> calcium ion parameters are transferable to a bound calcium.
>>
>> -Dan
>>
>> On Thu, Feb 28, 2019 at 7:24 AM Sunita Patel <sunita.patel.cbs.ac.in>
>> wrote:
>>>
>>> Dear David,
>>>
>>> I could generate topology and coordinate for Ca2+ bound protein with
>> amber
>>> 18, simply by sourcing "source leaprc.water.tip3p".
>>> I could not find "desc" command in the "bin" folder. I wanted to verify
>> the
>>> presence of calcium ions.
>>>
>>> This is how my tleap file looks.
>>> -----------------
>>> source leaprc.ff99SB
>>> source leaprc.water.tip3p
>>> set default PBradii mbondi2
>>> m = loadpdb AH_noH.pdb
>>> saveamberparm m AH_noH.prmtop AH_noH.inpcrd
>>> quit
>>> ----------------
>>> I will do REMD using Generalized Born (GB-OBC; igb=5) solvent model as it
>>> is for comparison purpose.
>>> Is it ok to simulate ion bound protein using GB-OBC model?
>>>
>>> Thank you so much for your help.
>>>
>>> With best regards,
>>> Sunita
>>>
>>> On Tue, Feb 12, 2019 at 7:56 PM David Case <david.case.rutgers.edu>
>> wrote:
>>>
>>>> On Tue, Feb 12, 2019, Sunita Patel wrote:
>>>>
>>>>> Can you please provide some links. I was thinking it would be straight
>>>>> forward like protein atom types.
>>>>
>>>> It *is* straightforward, although I agree that the manual section on
>>>> ions is more complex than it needs to be. Once you select a water
>> model
>>>> (via "source leaprc.water.xxxx"), monoatomic ions for that model are
>>>> automatically loaded as well. The exact parameters used are printed to
>>>> the screen when you load a water file.
>>>>
>>>> You can use the "desc" command in tleap to see which ions are present.
>>>> Following the PDB standard, the residue and atom name for calcium2+ are
>>>> both "CA". So make sure your input PDB file labels calcium as CA, and
>> you
>>>> should be fine.
>>>>
>>>> [Aside: the ff99SB force field is way out of date. If you are not
>> using
>>>> AmberTools18, you should upgrade to that version, and use ff14SB for
>>>> proteins.]
>>>>
>>>> [Aside to developers: the "Ions" section of the Reference Manual is
>>>> written only for some hypothetical super-expert who wants to know
>>>> details of ion parameters we no longer use. Can someone add an opening
>>>> paragraph describing what users are actually supposed to do in
>> practice,
>>>> i.e. that the water leaprc files include ions, and that the recommended
>>>> parameters are indentified there?]
>>>>
>>>> ...good luck....dac
>>>>
>>>>
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>>>>
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Received on Sat Mar 02 2019 - 19:30:02 PST
