[gmx-users] topology
RAHUL SURESH
drrahulsuresh at gmail.com
Thu Mar 2 14:23:00 CET 2017
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
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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
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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
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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
>
> * For (un)subscribe requests visit
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>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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