[gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

[Justin Lemkul]

On 12/18/19 6:40 AM, Quin K wrote:
> I generated ligand topology using parachem website, I didn't do any
> adjustments after, just used it as it is.

What do the penalty scores tell you about the quality of the parameters?

-Justin

> On Tue, 17 Dec 2019, 1:11 pm Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 12/15/19 1:18 PM, Quin K wrote:
>>> Hi
>>> Thank you!!!
>>>
>>> Let's say during restraining of ligand, if I increased  the -fc value to
>>> 10000 (i had 1000) or higher and equilibrated it for longer time like 1
>> or
>>> 2 ns (I had 100ps), would it help?
>> Possibly.
>>
>>> Also would  restraining the protein and ligand independently help?
>>> Or is generating a better ligand topology the only way to solve this
>> issue?
>>
>> It depends on how you validated the ligand topology. Do you have
>> evidence that it is of sufficiently high quality?
>>
>> -Justin
>>
>>> Thanks in advance.
>>> Regards
>>>
>>> On Sun, Dec 15, 2019 at 11:07 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 12/15/19 11:47 AM, Quin K wrote:
>>>>> Hi All,
>>>>>
>>>>> Further to following email, i just noted that the ligand has detached
>>>> from
>>>>> binding site.
>>>>> Is there a way to prevent this from happening?
>>>>> It happened to me once before with the same complex.
>>>> If the ligand is dissociating on a time scale that it shouldn't (e.g.
>>>> you expect it should stay bound), that suggests the ligand topology is
>>>> insufficiently accurate, arising from interactions with the protein that
>>>> are too weak and/or interactions with water that are too strong.
>>>>
>>>>> Doesn't boundary conditions prevent ligand from detaching from binding
>>>> site
>>>>> in protein during MD simulation?
>>>> No, PBC does not do this. A periodic system contains copies of whatever
>>>> is happening in the central image.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================