[gmx-users] protein ligand simulation
Justin Lemkul
jalemkul at vt.edu
Wed Apr 20 03:27:13 CEST 2016
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:
>>>>>
>>>>> [image: Boxbe] <https://www.boxbe.com/overview> This message is
>>>>> eligible
>>>>>
>>>>>> for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule
>>>>>> <
>>>>>>
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>>>>>>>
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>>>>>>
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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.
-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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