[gmx-users] topology
RAHUL SURESH
drrahulsuresh at gmail.com
Wed Mar 1 20:19:04 CET 2017
Dear Justin
What is the error here?
I don't understand it.
Can you be little more precise?
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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>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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