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

[Justin Lemkul]

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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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