[gmx-users] Charge on drug

[tasneem kausar]

Thank you
I have generated the itp file from ATB. It works fine.


On Wed, Dec 21, 2016 at 7:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/19/16 1:23 PM, tasneem kausar wrote:
>
>> Thank you for reply
>> What type of refinements are needed in topolgy file.
>> I have created the topology file from pdb file. Mol2 was converted into
>> pdb
>> and sdf of pubchem was converted into mol2.
>> So sdf to mol2 to pdb.
>> And please suggest me the right choice of server for itp file generation.
>>
>>
> Check the bond length parameters and make sure your coordinate file
> matches the order of the atoms in the topology.  Don't ignore warnings from
> grompp.
>
> -Justin
>
>
> Thanks in advance
>>
>> On 19 Dec 2016 18:31, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>>
>>> On 12/19/16 5:31 AM, tasneem kausar wrote:
>>>
>>>>
>>>> Thanks for reply
>>>>
>>>> I have visualized solvate.gro and em.gro. Some bonds that are not
>>>> present
>>>> in box.gro is seen in em.gro.
>>>> I am giving you the link of the file to visualize.
>>>> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
>>>> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
>>>>
>>>
>>>
>>> You have an amide group that distorts, bringing the carbonyl C closer to
>>>
>> the amide proton, which VMD then fictitiously assigns as a C-H bond.  The
>> C-N bond is much too short.  This suggests your topology is of
>> insufficient
>> quality for doing simulations and requires refinement.  There is, of
>> course, no actual bond there, as Mark has pointed out.  Visualization
>> software tries to guess where bonds should be based on interatomic
>> distances.  The topology is definitive. What you see on your screen is
>> not.
>>
>>>
>>>
>>> I addition to that I have done energy minimization multiple times with
>>>> steepest decent and conjugate gradient method. Potential energy value is
>>>> negative in every minimization. When I am trying position restrain core
>>>> dump with multiple lincs warning occurs.
>>>>
>>>
>>>
>>> Your topology needs work.  It will not be stable for any simulation.
>>>
>>> -Justin
>>>
>>>
>>> Please tell me how this problem would be resolved
>>>>
>>>> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abraham at gmail.com
>>>> >
>>>> wrote:
>>>>
>>>> Hi,
>>>>>
>>>>> Your energy minimization literally cannot create bonds because those
>>>>> are
>>>>> already defined by your topology. See
>>>>>
>>>>> http://www.gromacs.org/Downloads/Related_Software/Visualizat
>> ion_Software#
>>
>>> Topology_bonds_vs_Rendered_bonds
>>>>> for what's probably going on.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausar12 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Dear All
>>>>>>
>>>>>>
>>>>>> I am using Acpype server to generate topology file of drug molecule to
>>>>>> perform protein drug MD simulation. Acpype have generated the itp file
>>>>>>
>>>>>
>>>>> and
>>>>>
>>>>>>
>>>>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>>>>>>
>>>>>
>>>>> software
>>>>>
>>>>>>
>>>>>> using amber99sb force field. When I have done energy minimization some
>>>>>> unwanted bonds are formed in drug molecule. So the position restraint
>>>>>>
>>>>> is
>>
>>> not able to execute. The problem is due to the unusual bond in drug
>>>>>>
>>>>> atom.
>>
>>> When I used the itp file of PRODRG server position restraint goes
>>>>>> successfully. I have used the gromos54a7 ff. But there is problem with
>>>>>>
>>>>>
>>>>> the
>>>>>
>>>>>>
>>>>>> charge present on the atom that comes from PRODRG.
>>>>>>
>>>>>> Please tell me how charge on the atom can be corrected in itp file of
>>>>>> PRODRG.  How the problem in energy minimization with the Acpype itp
>>>>>>
>>>>> will
>>
>>>
>>>>> be
>>>>>
>>>>>>
>>>>>> resolved.
>>>>>>
>>>>>> Thanks in Advance
>>>>>> With Regards
>>>>>> Tasneem
>>>>>> --
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>>>>>
>>> --
>>> ==================================================
>>>
>>> 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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> --
> ==================================================
>
> 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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