[gmx-users] topology
RAHUL SURESH
drrahulsuresh at gmail.com
Thu Mar 2 05:23:12 CET 2017
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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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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>>>
>>
>>
>>
> --
> ==================================================
>
> 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
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>
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>
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>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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