[gmx-users] topology
Justin Lemkul
jalemkul at vt.edu
Tue Feb 28 21:28:28 CET 2017
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
>>
>> ==================================================
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>> 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
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