[gmx-users] protein ligand simulation
bharat gupta
bharat.85.monu at gmail.com
Wed Apr 20 09:32:04 CEST 2016
On Wed, Apr 20, 2016 at 10:27 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
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> On 4/19/16 9:22 PM, bharat gupta wrote:
>
>> 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:
>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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 ??
>>
>>
> Force fields with a strong connection to QM always start by deriving
> parameters from the optimized geometry. For GROMOS, where the
> parametrization is done very empirically, I don't how important this will
> be. You can, of course, generate two topologies and compare them. What
> you should *not* do is use the optimized geometry as it has been minimized
> in vacuo and therefore no longer is likely to have any resemblance to the
> structure that is bound to your protein. For a trisaccharide, which is
> very flexible, this is particularly important.
>
> 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 ?
>>
>>
> If nothing else, it's all derived from simple geometric measurements that
> can be made using GROMACS utilities.
>
Thanks, but could you provide some pointers for such calculations??
>
> -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
>
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