[gmx-users] topology
RAHUL SURESH
drrahulsuresh at gmail.com
Thu Mar 2 14:25:32 CET 2017
How to edit the .hdb file
On Thu, Mar 2, 2017 at 6:52 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:
> I can manually parametrize my topology but to parametrize Hydrogen atoms
> goes too tedious.
> There must be any easy way.?
>
> On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/2/17 2:51 AM, Subashini .K wrote:
>>
>>> Did you try PRODRG server?
>>>
>>>
>> Broken record time: the quality of PRODRG topologies is very low. One
>> should always manually reparametrize the molecule, or use better servers
>> like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if
>> the goal is an OPLS-AA topology.
>>
>> -Justin
>>
>>
>>
>>>
>>> ________________________________
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of RAHUL
>>> SURESH <drrahulsuresh at gmail.com>
>>> Sent: Thursday, March 2, 2017 9:53 AM
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] topology
>>>
>>> Dear Justin
>>>
>>> Is there anything I can do to make this job easier?
>>>
>>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>>>>
>>>> Dear Justin
>>>>>
>>>>> What is the error here?
>>>>> I don't understand it.
>>>>> Can you be little more precise?
>>>>>
>>>>>
>>>>> The long and short of it TopolGen is very crudely coded and atom order
>>>> matters because the script makes a lot of assumptions. Your input PDB
>>>> file
>>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
>>>> out what any of the actual functional groups are, so you get basically
>>>> default atom types for everything.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>>>>>>
>>>>>> This is my itp file(only a part)
>>>>>>
>>>>>>>
>>>>>>> I have highlighted two errors.. there are 19 such errors.
>>>>>>> If I can know the reason for the error exactly it would be of a great
>>>>>>> help
>>>>>>> to me.
>>>>>>>
>>>>>>>
>>>>>>> TopolGen relies on atom ordering to guess what the proper parameters
>>>>>>>
>>>>>> should be. It's pretty limited in what it can do. A coordinate file
>>>>>> that
>>>>>> simply groups atoms by element is going to produce a totally garbage
>>>>>> topology, unfortunately.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> [ atoms ]
>>>>>>
>>>>>>> ; nr type resnr residue atom cgnr charge mass
>>>>>>> typeB chargeB massB
>>>>>>> 1 opls_154 1 UNK O 0 -0.580921
>>>>>>> 15.99940
>>>>>>> 2 opls_154 1 UNK O 0 -0.635654
>>>>>>> 15.99940
>>>>>>> 3 opls_516 1 UNK C 1 -0.112257
>>>>>>> 12.01100
>>>>>>> 4 opls_516 1 UNK C 2 -0.163224
>>>>>>> 12.01100
>>>>>>> 5 opls_516 1 UNK C 3 0.228741
>>>>>>> 12.01100
>>>>>>> 6 opls_516 1 UNK C 4 -0.304756
>>>>>>> 12.01100
>>>>>>> 7 opls_516 1 UNK C 5 -0.312217
>>>>>>> 12.01100
>>>>>>> 8 opls_145 1 UNK C 6 0.120569
>>>>>>> 12.01100
>>>>>>> 9 opls_145 1 UNK C 7 0.151897
>>>>>>> 12.01100
>>>>>>> 10 opls_145 1 UNK C 8 0.231044
>>>>>>> 12.01100
>>>>>>> 11 opls_516 1 UNK C 9 -0.401751
>>>>>>> 12.01100
>>>>>>> 12 opls_516 1 UNK C 10 -0.403094
>>>>>>> 12.01100
>>>>>>> 13 opls_145 1 UNK C 11 -0.150352
>>>>>>> 12.01100
>>>>>>> 14 opls_145 1 UNK C 12 0.193129
>>>>>>> 12.01100
>>>>>>> 15 opls_145 1 UNK C 13 -0.161115
>>>>>>> 12.01100
>>>>>>> 16 opls_516 1 UNK C 14 -0.471874
>>>>>>> 12.01100
>>>>>>> 17 opls_145 1 UNK C 15 0.100725
>>>>>>> 12.01100
>>>>>>> 18 opls_145 1 UNK C 16 -0.153943
>>>>>>> 12.01100
>>>>>>> 19 opls_516 1 UNK C 17 -0.330577
>>>>>>> 12.01100
>>>>>>> 20 opls_516 1 UNK C 18 -0.229875
>>>>>>> 12.01100
>>>>>>> 21 opls_135 1 UNK C 19 -0.229884
>>>>>>> 12.01100
>>>>>>> 22 opls_135 1 UNK C 20 -0.237230
>>>>>>> 12.01100
>>>>>>> 23 opls_135 1 UNK C 21 -0.404861
>>>>>>> 12.01100
>>>>>>> 24 opls_140 1 UNK H 21 0.135257
>>>>>>> 1.00800
>>>>>>> 25 opls_140 1 UNK H 21 0.154010
>>>>>>> 1.00800
>>>>>>> 26 opls_140 1 UNK 2H 21 0.142643
>>>>>>> 1.00800
>>>>>>> 27 opls_140 1 UNK 1H 21 0.133623
>>>>>>> 1.00800
>>>>>>> 28 opls_140 1 UNK 2H 21 0.137323
>>>>>>> 1.00800
>>>>>>> 29 opls_140 1 UNK 1H 21 0.167475
>>>>>>> 1.00800
>>>>>>> 30 opls_140 1 UNK 1H 21 0.135348
>>>>>>> 1.00800
>>>>>>> 31 opls_140 1 UNK 2H 21 0.153851
>>>>>>> 1.00800
>>>>>>> 32 opls_140 1 UNK 3H 21 0.138487
>>>>>>> 1.00800
>>>>>>> 33 opls_140 1 UNK 1H 21 0.137087
>>>>>>> 1.00800
>>>>>>> 34 opls_140 1 UNK 2H 21 0.146500
>>>>>>> 1.00800
>>>>>>> 35 opls_140 1 UNK 3H 21 0.148972
>>>>>>> 1.00800
>>>>>>> 36 opls_140 1 UNK H 21 0.103605
>>>>>>> 1.00800
>>>>>>> 37 opls_140 1 UNK H 21 0.127061
>>>>>>> 1.00800
>>>>>>> 38 opls_140 1 UNK 1H 21 0.143100
>>>>>>> 1.00800
>>>>>>> 39 opls_140 1 UNK 2H 21 0.137525
>>>>>>> 1.00800
>>>>>>> 40 opls_140 1 UNK 3H 21 0.140672
>>>>>>> 1.00800
>>>>>>> 41 opls_140 1 UNK H 21 0.106416
>>>>>>> 1.00800
>>>>>>> 42 opls_140 1 UNK 1H 21 0.134610
>>>>>>> 1.00800
>>>>>>> 43 opls_140 1 UNK 2H 21 0.126890
>>>>>>> 1.00800
>>>>>>> 44 opls_140 1 UNK 2H 21 0.132690
>>>>>>> 1.00800
>>>>>>> 45 opls_140 1 UNK 1H 21 0.124796
>>>>>>> 1.00800
>>>>>>> 46 opls_140 1 UNK H 21 0.371894
>>>>>>> 1.00800
>>>>>>> 47 opls_140 1 UNK 1H 21 0.120642
>>>>>>> 1.00800
>>>>>>> 48 opls_140 1 UNK 2H 21 0.117792
>>>>>>> 1.00800
>>>>>>> 49 opls_140 1 UNK 2H 21 0.125342
>>>>>>> 1.00800
>>>>>>> 50 opls_140 1 UNK 1H 21 0.122930
>>>>>>> 1.00800
>>>>>>> 51 opls_140 1 UNK 1H 21 0.130012
>>>>>>> 1.00800
>>>>>>> 52 opls_140 1 UNK 2H 21 0.129674
>>>>>>> 1.00800
>>>>>>> 53 opls_140 1 UNK 3H 21 0.131255
>>>>>>> 1.00800
>>>>>>>
>>>>>>> [ bonds ]
>>>>>>> ; ai aj funct
>>>>>>> 1 5 1 ; O C
>>>>>>> 1 10 1 ; O C
>>>>>>> 2 14 1 ; O C
>>>>>>> *2 46 1 ; O H*
>>>>>>>
>>>>>>> 3 4 1 ; C C
>>>>>>> 3 5 1 ; C C
>>>>>>> 3 6 1 ; C C
>>>>>>> 3 24 1 ; C H
>>>>>>> 4 7 1 ; C C
>>>>>>> 4 8 1 ; C C
>>>>>>> 4 25 1 ; C H
>>>>>>> 5 11 1 ; C C
>>>>>>> 5 12 1 ; C C
>>>>>>> 6 13 1 ; C C
>>>>>>> 6 26 1 ; C 2H
>>>>>>> 6 27 1 ; C 1H
>>>>>>> 7 9 1 ; C C
>>>>>>> 7 28 1 ; C 2H
>>>>>>> 7 29 1 ; C 1H
>>>>>>> 8 10 1 ; C C
>>>>>>> 8 14 1 ; C C
>>>>>>> 9 13 1 ; C C
>>>>>>> 9 16 1 ; C C
>>>>>>> 10 15 1 ; C C
>>>>>>> 11 30 1 ; C 1H
>>>>>>> 11 31 1 ; C 2H
>>>>>>> 11 32 1 ; C 3H
>>>>>>> 12 33 1 ; C 1H
>>>>>>> 12 34 1 ; C 2H
>>>>>>> 12 35 1 ; C 3H
>>>>>>> *13 36 1 ; C H*
>>>>>>>
>>>>>>> 14 18 1 ; C C
>>>>>>> 15 17 1 ; C C
>>>>>>> 15 37 1 ; C H
>>>>>>> 16 38 1 ; C 1H
>>>>>>> 16 39 1 ; C 2H
>>>>>>> 16 40 1 ; C 3H
>>>>>>> 17 18 1 ; C C
>>>>>>> 17 19 1 ; C C
>>>>>>> 18 41 1 ; C H
>>>>>>> 19 20 1 ; C C
>>>>>>> 19 42 1 ; C 1H
>>>>>>> 19 43 1 ; C 2H
>>>>>>> 20 21 1 ; C C
>>>>>>> 20 44 1 ; C 2H
>>>>>>> 20 45 1 ; C 1H
>>>>>>> 21 22 1 ; C C
>>>>>>> 21 47 1 ; C 1H
>>>>>>> 21 48 1 ; C 2H
>>>>>>> 22 23 1 ; C C
>>>>>>> 22 49 1 ; C 2H
>>>>>>> 22 50 1 ; C 1H
>>>>>>> 23 51 1 ; C 1H
>>>>>>> 23 52 1 ; C 2H
>>>>>>> 23 53 1 ; C 3H
>>>>>>>
>>>>>>> On Tue, Feb 28, 2017 at 3:57 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 2/27/17 12:49 AM, RAHUL SURESH wrote:
>>>>>>>>
>>>>>>>> I am explaining my issues regarding complex simulation.
>>>>>>>>
>>>>>>>>
>>>>>>>>> I have 200ns conformer(OPLS FF)
>>>>>>>>>
>>>>>>>>> I have generated my ligand gro and itp file.(Using topolgen1_1)
>>>>>>>>>
>>>>>>>>> I have edited my protein gro file and made it into complex file as
>>>>>>>>> per
>>>>>>>>> the
>>>>>>>>> tutorials.
>>>>>>>>>
>>>>>>>>> I have made changes to my topol.top file.
>>>>>>>>>
>>>>>>>>> Now in my command for em.mdp I am getting 19 errors stating "NO
>>>>>>>>> DEFAULT
>>>>>>>>> BOND TYPE, ANGLE TYPE, ETC."
>>>>>>>>>
>>>>>>>>> Can you guide me with this?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> This means the atom type assignment makes reference to bonded
>>>>>>>>> parameters
>>>>>>>>>
>>>>>>>>> that don't exist. That means one of two things: (1) either the
>>>>>>>> atom
>>>>>>>> type
>>>>>>>> assignment is incorrect, requiring manual correction (as the script
>>>>>>>> warns
>>>>>>>> you, as it makes a lot of assumptions and is therefore rather dumb
>>>>>>>> sometimes) or (2) you simply have a molecule for which parameters do
>>>>>>>> not
>>>>>>>> exist, requiring manual parametrization. For OPLS-AA, this
>>>>>>>> requires QM
>>>>>>>> calculations to get things like equilibrium geometries, vibrational
>>>>>>>> frequencies, and dihedral potential energy scans.
>>>>>>>>
>>>>>>>>
>>>>>>>> -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
>>>>>>>>
>>>>>>> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
>>> http://mackerell.umaryland.edu/~jalemkul>
>>>
>>> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland
>>> .edu/~jalemkul>
>>> mackerell.umaryland.edu
>>> Welcome to my site! To learn more about me and the work I am doing,
>>> please use the navigation links above.
>>>
>>>
>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
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>>>>>>>> or
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> 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!
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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!
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>>>>
>>>>
>>>
>>>
>>> --
>>> *Regards,*
>>> *Rahul Suresh*
>>> *Research Scholar*
>>> *Bharathiar University*
>>> *Coimbatore*
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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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
>>
>> ==================================================
>> --
>> 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
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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