[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Justin Lemkul
jalemkul at vt.edu
Tue Jul 11 19:04:14 CEST 2017
On 7/11/17 2:46 AM, Akash Ranjan wrote:
> Sir,
>
> I am facing difficulty in making topology for a simple molecule using CHARMM36
> but i am facing certain difficulty in that such as
>
> (a)Warning: Long Bond (3-10 = 0.566378 nm)
> Warning: Long Bond (3-4 = 0.426475 nm)
> Warning: Long Bond (4-16 = 0.59 nm)
> Warning: Long Bond (4-11 = 0.671583 nm)
> Warning: Long Bond (5-6 = 0.428864 nm)
> Warning: Short Bond (5-7 = 0.044 nm)
> Warning: Long Bond (7-8 = 0.648229 nm)
> Warning: Long Bond (8-20 = 0.539527 nm)
> Warning: Long Bond (9-21 = 0.849567 nm)
> Warning: Long Bond (10-22 = 0.584145 nm)
> Warning: Long Bond (11-23 = 0.637749 nm)
>
>
> (b)
> ERROR 4 [file topol.top, line 76]:
> No default Bond types
>
>
>
>
> ERROR 7 [file topol.top, line 169]:
> No default U-B types
>
>
> ERROR 19 [file topol.top, line 202]:
> No default Proper Dih. types
>
The missing parameters mean your atom type assignments are incorrect.
> Here is mine rtp enteries.can you suggest me how to correct t?
>
>
> [ UNK ]
> [ atoms ]
> C1 CC3161 12.01100 1
> C2 CC3161 12.01100 2
> C3 CC3161 12.01100 3
> C4 CC3162 12.01100 4
> C5 CC3163 12.01100 5
> O6 OC3C61 -0.400 6
> C7 CC3161 12.01100 7
> O8 OC311 -0.650 8
> O9 OC311 -0.650 9
> O10 OC311 -0.650 10
> O11 OC311 -0.650 11
> O12 OC311 -0.650 12
> H13 HCA1 1.00800 13
> H14 HCA1 1.00800 14
> H15 HCA1 1.00800 15
> H16 HCA1 1.00800 16
> H17 HCA1 1.00800 17
> H18 HCA1 1.00800 18
> H19 HCA1 1.00800 19
> H20 HX 0.090 20
> H21 HX 0.090 21
> H22 HX 0.090 22
> H23 HX 0.090 23
> H24 HX 0.090 24
>
You have a mix of charges and masses in the column that should only be charges,
so this is a fundamentally broken entry.
>
> [ bonds ]
> C1 H13
> C1 O12
> C1 C5
> C1 C2
> C2 H14
> C2 O9
> C2 C3
> C3 H15
> C3 O10
> C3 C4
> C4 H16
> C4 O11
> C4 O6
> C5 O6
> C5 C7
> C5 H17
> C7 H18
> C7 H19
> C7 O8
> O8 H20
> O9 H21
> O10 H22
> O11 H23
> O12 H24
>
> PDB file:-
>
Have you visualized these coordinates? The format is totally broken so this is
what pdb2gmx is complaining about. The structure is complete nonsense.
-Justin
> HEADER PROTEIN 06-JUL-17 NONE
> TITLE NULL
> COMPND MOLECULE: ads1.mol
> SOURCE NULL
> KEYWDS NULL
> EXPDTA NULL
> AUTHOR Marvin
> ATOM 1 C1 UNK 0 2.462 -3.244 0.792 1.00 0.00 C
> ATOM 2 C2 UNK 0 2.766 -4.727 0.446 1.00 0.00 C
> ATOM 3 C3 UNK 0 1.464 -5.574 0.403 1.00 0.00 C
> ATOM 4 C4 UNK 0 0.378 -4.893 -0.473 1.00 0.00 C
> ATOM 5 C5 UNK 0 1.343 -2.682 -0.137 1.00 0.00 C
> ATOM 6 O6 UNK 0 0.167 -3.523 -0.076 1.00 0.00 O
> ATOM 7 C7 UNK 0 0.903 -1.252 0.257 1.00 0.00 C
> ATOM 8 O8 UNK 0 -0.118 -0.796 -0.628 1.00 0.00 O
> ATOM 9 O9 UNK 0 3.663 -5.266 1.418 1.00 0.00 O
> ATOM 10 O10 UNK 0 1.748 -6.880 -0.095 1.00 0.00 O
> ATOM 11 O11 UNK 0 0.692 -4.976 -1.864 1.00 0.00 O
> ATOM 12 O12 UNK 0 3.652 -2.465 0.678 1.00 0.00 O
> HETATM 13 H13 UNK 0 2.111 -3.189 1.801 1.00 0.00 H
> HETATM 14 H14 UNK 0 3.215 -4.763 -0.524 1.00 0.00 H
> HETATM 15 H15 UNK 0 1.084 -5.651 1.400 1.00 0.00 H
> HETATM 16 H16 UNK 0 -0.535 -5.428 -0.314 1.00 0.00 H
> HETATM 17 H17 UNK 0 1.761 -2.663 -1.122 1.00 0.00 H
> HETATM 18 H18 UNK 0 1.744 -0.593 0.198 1.00 0.00 H
> HETATM 19 H19 UNK 0 0.522 -1.264 1.257 1.00 0.00 H
> HETATM 20 H20 UNK 0 0.223 -0.784 -1.536 1.00 0.00 H
> HETATM 21 H21 UNK 0 3.249 -5.230 2.295 1.00 0.00 H
> HETATM 22 H22 UNK 0 2.093 -6.813 -0.999 1.00 0.00 H
> HETATM 23 H23 UNK 0 1.518 -4.498 -2.038 1.00 0.00 H
> HETATM 24 H24 UNK 0 3.980 -2.507 -0.234 1.00 0.00 H
> CONECT 1 2 5 12 13
> CONECT 2 1 3 9 14
> CONECT 3 2 4 10 15
> CONECT 4 3 6 11 16
> CONECT 5 1 6 7 17
> CONECT 6 4 5
> CONECT 7 5 8 18 19
> CONECT 8 7 20
> CONECT 9 2 21
> CONECT 10 3 22
> CONECT 11 4 23
> CONECT 12 1 24
> CONECT 13 1
> CONECT 14 2
> CONECT 15 3
> CONECT 16 4
> CONECT 17 5
> CONECT 18 7
> CONECT 19 7
> CONECT 20 8
> CONECT 21 9
> CONECT 22 10
> CONECT 23 11
> CONECT 24 12
> MASTER 0 0 0 0 0 0 0 0 24 0 24 0
> END
>
>
> Akash
>
> Thanks
>
>
--
==================================================
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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