[gmx-users] topology
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Feb 28 09:24:39 CET 2017
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.
[ 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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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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