[gmx-users] protein ligand simulation
bharat gupta
bharat.85.monu at gmail.com
Wed Apr 20 03:22:26 CEST 2016
On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/19/16 9:08 PM, bharat gupta wrote:
>
>> On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/19/16 9:01 PM, bharat gupta wrote:
>>>
>>> Thanks for your prompt response.
>>>>
>>>> On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>> [image: Boxbe] <https://www.boxbe.com/overview> This message is
>>>> eligible
>>>>
>>>>> for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule
>>>>> <
>>>>>
>>>>> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DnqH3v%252FMS7bSEnB454b3Ikkoit6nvnpvzcrlHpGyN%252FWIOKBoecFU4zltFf7D%252FYHe8BMrH1ORmgTsP4gtx3fq3yEa336uM2rOLjzwPj4EjjwW0R0s7UGq4mdNAYkzXlGsJnrJrUQmI2jI%253D%26key%3DaZka6hEojvmt2tNDVLAPxoi7nhM7mRhpdu5MiY96JP8%253D&tc_serial=25130648872&tc_rand=1182875792&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>>>>>
>>>>>>
>>>>>> | More info
>>>>> <
>>>>>
>>>>> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=25130648872&tc_rand=1182875792&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 4/19/16 8:28 PM, bharat gupta wrote:
>>>>>
>>>>> Hi Justin,
>>>>>
>>>>>>
>>>>>> Here's the link for following files: complex.gro, CT3.itp (ligand
>>>>>> topology), CT3.gro (ligand coordinates) and topology.top.
>>>>>>
>>>>>>
>>>>>>
>>>>>> https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA&usp=drive_web
>>>>>>
>>>>>> When I run make_ndx command using the solvated complex file
>>>>>> (solv.gro),
>>>>>> I
>>>>>> don't find the ligand in any of the groups. Here's the output of that
>>>>>> command:
>>>>>>
>>>>>> Command line:
>>>>>> make_ndx -f solv.gro -o index.ndx
>>>>>>
>>>>>>
>>>>>> Reading structure file
>>>>>> Going to read 0 old index file(s)
>>>>>> Analysing residue names:
>>>>>> There are: 368 Protein residues
>>>>>> There are: 14227 Water residues
>>>>>> Analysing Protein...
>>>>>>
>>>>>> 0 System : 46221 atoms
>>>>>> 1 Protein : 3540 atoms
>>>>>> 2 Protein-H : 2746 atoms
>>>>>> 3 C-alpha : 367 atoms
>>>>>> 4 Backbone : 1101 atoms
>>>>>> 5 MainChain : 1470 atoms
>>>>>> 6 MainChain+Cb : 1795 atoms
>>>>>> 7 MainChain+H : 1826 atoms
>>>>>> 8 SideChain : 1714 atoms
>>>>>> 9 SideChain-H : 1276 atoms
>>>>>> 10 Prot-Masses : 3540 atoms
>>>>>> 11 non-Protein : 42681 atoms
>>>>>> 12 Water : 42681 atoms
>>>>>> 13 SOL : 42681 atoms
>>>>>> 14 non-Water : 3540 atoms
>>>>>>
>>>>>>
>>>>>> Then solv.gro clearly doesn't contain your ligand; you haven't
>>>>>>
>>>>> constructed
>>>>> the system properly.
>>>>>
>>>>> I have did exactly what the tutorial mentioned about ligand topology
>>>>>
>>>> preparation. I have sent you the files as well (complex.gro, topol.top).
>>>> I
>>>> did this preparation at least 2-3 times but every time I don't get the
>>>> ligand. Did you have a look at these files ??
>>>>
>>>>
>>>> Your problem is with solv.gro, and since none of the files provided are
>>> solv.gro, they are not relevant.
>>>
>>> Here's the link.
>> https://drive.google.com/open?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA
>>
>>
> Apparently you added your ligand to residuetypes.dat and called it
> Protein. You have 3540 atoms that are identified as Protein by make_ndx;
> that encompasses the actual protein and the ligand. You can still select
> the ligand by its residue name or number, but it won't appear in any
> selection lists as a separate entry if you tell GROMACS tools to consider
> it protein. This will cause issues with some analysis tools like do_dssp
> and gmx chi.
Okay, but it means that I have done something wrong while preparing the
files for the ligand. Actually, I didn't add the ligand to
residuetypes.dat, I did exactly what the protein-ligand tutorial mentioned.
Now, I got to know where the error is. I should rename my ligand instead of
using CT3. As, CT3 is already present in the residuetypes.dat file.
Atlast, after spending 2 horrible days at this, I can move forward with the
simulation.
Regarding the ligand parameters after optimization (from ATB server), I
already checked the post you mentioned earlier. But, my doubt is whether is
it reasonable to use the unoptimized ligand for simulation ??
Also, I am using gromacs v 5.0.4 and I want to use the tool g_puckering
which was written for v 4.x.x. I am not able to compile that, so could you
recommend so other tool to calculate cremer pople parameters for sugar
puckering, as my ligand is a trisaccharide ?
Thanks Justin
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> 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.
>
--
*Best Regards*
Bharat
More information about the gromacs.org_gmx-users
mailing list