[gmx-users] CHARMM-GUI files give error in Gromacs
Justin Lemkul
jalemkul at vt.edu
Fri Sep 2 16:31:13 CEST 2016
On 9/2/16 10:28 AM, gozde ergin wrote:
> Dear all,
>
> I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid.
> After that I used genbox command of gromacs and add some water molecules.
> When I try to run I get 100 Errors saying :
>
> No default bond types, No default U-B types, No default Proper Dih. types, No default Improper Dih. types.
>
> All these errors are related to .itp file. However .itp files seems correct:
>
> Any help would be appreciated. Thanks.
>
>
CHARMM-GUI provides a self-contained force field file that will have everything
you need. It is a subset of the full CHARMM force field plus any parameters
that are newly introduced by your non-standard molecule. Are you using only
files directly from CHARMM-GUI, without modification, or are you trying to do
something else?
-Justin
> ;;
> ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
> ;;
> ;; psf2itp_mol.py
> ;;
> ;; Correspondance:
> ;; j712l362 at ku.edu or wonpil at ku.edu
> ;;
> ;; GROMACS topology file for LIG
> ;;
>
>
> [ moleculetype ]
> ; name nrexcl
> LIG 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 CG3C41 1 LIG C2 1 -0.087 12.0110 ; qtot -0.087
> 2 CG3C41 1 LIG C1 2 -0.046 12.0110 ; qtot -0.133
> 3 HGA1 1 LIG H1 3 0.090 1.0080 ; qtot -0.043
> 4 CG3C41 1 LIG C3 4 -0.038 12.0110 ; qtot -0.081
> 5 CG2O5 1 LIG C8 5 0.388 12.0110 ; qtot 0.307
> 6 HGA1 1 LIG H2 6 0.090 1.0080 ; qtot 0.397
> 7 OG2D3 1 LIG O1 7 -0.481 15.9994 ; qtot -0.084
> 8 CG331 1 LIG C10 8 -0.229 12.0110 ; qtot -0.313
> 9 HGA3 1 LIG H14 9 0.090 1.0080 ; qtot -0.223
> 10 HGA3 1 LIG H15 10 0.090 1.0080 ; qtot -0.133
> 11 HGA3 1 LIG H13 11 0.090 1.0080 ; qtot -0.043
> 12 CG3C41 1 LIG C4 12 -0.178 12.0110 ; qtot -0.221
> 13 HGA2 1 LIG H4 13 0.090 1.0080 ; qtot -0.131
> 14 HGA2 1 LIG H3 14 0.090 1.0080 ; qtot -0.041
> 15 CG331 1 LIG C6 15 -0.248 12.0110 ; qtot -0.289
> 16 HGA3 1 LIG H10 16 0.090 1.0080 ; qtot -0.199
> 17 HGA3 1 LIG H9 17 0.090 1.0080 ; qtot -0.109
> 18 HGA3 1 LIG H8 18 0.090 1.0080 ; qtot -0.019
> 19 CG331 1 LIG C5 19 -0.248 12.0110 ; qtot -0.267
> 20 HGA3 1 LIG H6 20 0.090 1.0080 ; qtot -0.177
> 21 HGA3 1 LIG H7 21 0.090 1.0080 ; qtot -0.087
> 22 HGA3 1 LIG H5 22 0.090 1.0080 ; qtot 0.003
> 23 CG321 1 LIG C7 23 -0.207 12.0110 ; qtot -0.204
> 24 CG2O2 1 LIG C9 24 0.803 12.0110 ; qtot 0.599
> 25 HGA2 1 LIG H12 25 0.090 1.0080 ; qtot 0.689
> 26 HGA2 1 LIG H11 26 0.090 1.0080 ; qtot 0.779
> 27 OG2D1 1 LIG O3 27 -0.576 15.9994 ; qtot 0.203
> 28 OG311 1 LIG O2 28 -0.632 15.9994 ; qtot -0.429
> 29 HGP1 1 LIG H16 29 0.429 1.0080 ; qtot 0.000
>
> [ bonds ]
> ; ai aj funct b0 Kb
> 1 2 1
> 1 3 1
> 1 12 1
> 1 23 1
> 2 4 1
> 2 15 1
> 2 19 1
> 4 5 1
> 4 6 1
> 4 12 1
> 5 7 1
> 5 8 1
> 8 9 1
> 8 10 1
> 8 11 1
> 12 13 1
> 12 14 1
> 15 16 1
> 15 17 1
> 15 18 1
> 19 20 1
> 19 21 1
> 19 22 1
> 23 24 1
> 23 25 1
> 23 26 1
> 24 27 1
> 24 28 1
> 28 29 1
>
> [ pairs ]
> ; ai aj funct c6 c12
> 1 2 1
> 1 5 1
> 1 6 1
> 1 12 1
> 1 16 1
> 1 17 1
> 1 18 1
> 1 20 1
> 1 21 1
> 1 22 1
> 1 27 1
> 1 28 1
> 2 4 1
> 2 7 1
> 2 8 1
> 2 13 1
> 2 14 1
> 2 24 1
> 2 25 1
> 2 26 1
> 3 4 1
> 3 13 1
> 3 14 1
> 3 15 1
> 3 19 1
> 3 24 1
> 3 25 1
> 3 26 1
> 4 9 1
> 4 10 1
> 4 11 1
> 4 12 1
> 4 16 1
> 4 17 1
> 4 18 1
> 4 20 1
> 4 21 1
> 4 22 1
> 4 23 1
> 5 13 1
> 5 14 1
> 5 15 1
> 5 19 1
> 6 7 1
> 6 8 1
> 6 13 1
> 6 14 1
> 6 15 1
> 6 19 1
> 7 9 1
> 7 10 1
> 7 11 1
> 7 12 1
> 8 12 1
> 12 15 1
> 12 19 1
> 12 24 1
> 12 25 1
> 12 26 1
> 13 23 1
> 14 23 1
> 15 20 1
> 15 21 1
> 15 22 1
> 15 23 1
> 16 19 1
> 17 19 1
> 18 19 1
> 19 23 1
> 23 29 1
> 25 27 1
> 25 28 1
> 26 27 1
> 26 28 1
> 27 29 1
>
> [ angles ]
> ; ai aj ak funct th0 cth S0 Kub
> 2 1 3 5
> 2 1 12 5
> 2 1 23 5
> 3 1 12 5
> 3 1 23 5
> 12 1 23 5
> 1 2 4 5
> 1 2 15 5
> 1 2 19 5
> 4 2 15 5
> 4 2 19 5
> 15 2 19 5
> 2 4 5 5
> 2 4 6 5
> 2 4 12 5
> 5 4 6 5
> 5 4 12 5
> 6 4 12 5
> 4 5 7 5
> 4 5 8 5
> 7 5 8 5
> 5 8 9 5
> 5 8 10 5
> 5 8 11 5
> 9 8 10 5
> 9 8 11 5
> 10 8 11 5
> 1 12 4 5
> 1 12 13 5
> 1 12 14 5
> 4 12 13 5
> 4 12 14 5
> 13 12 14 5
> 2 15 16 5
> 2 15 17 5
> 2 15 18 5
> 16 15 17 5
> 16 15 18 5
> 17 15 18 5
> 2 19 20 5
> 2 19 21 5
> 2 19 22 5
> 20 19 21 5
> 20 19 22 5
> 21 19 22 5
> 1 23 24 5
> 1 23 25 5
> 1 23 26 5
> 24 23 25 5
> 24 23 26 5
> 25 23 26 5
> 23 24 27 5
> 23 24 28 5
> 27 24 28 5
> 24 28 29 5
>
> [ dihedrals ]
> ; ai aj ak al funct phi0 cp mult
> 3 1 2 4 9
> 3 1 2 15 9
> 3 1 2 19 9
> 12 1 2 15 9
> 12 1 2 19 9
> 2 1 12 4 9
> 2 1 12 13 9
> 2 1 12 14 9
> 3 1 12 4 9
> 3 1 12 13 9
> 3 1 12 14 9
> 2 1 23 24 9
> 2 1 23 25 9
> 2 1 23 26 9
> 3 1 23 24 9
> 3 1 23 25 9
> 3 1 23 26 9
> 12 1 23 24 9
> 12 1 23 25 9
> 12 1 23 26 9
> 4 2 1 12 9
> 4 2 1 23 9
> 15 2 1 23 9
> 19 2 1 23 9
> 1 2 4 5 9
> 1 2 4 6 9
> 1 2 4 12 9
> 1 2 15 16 9
> 1 2 15 17 9
> 1 2 15 18 9
> 4 2 15 16 9
> 4 2 15 17 9
> 4 2 15 18 9
> 1 2 19 20 9
> 1 2 19 21 9
> 1 2 19 22 9
> 4 2 19 20 9
> 4 2 19 21 9
> 4 2 19 22 9
> 15 2 19 20 9
> 15 2 19 21 9
> 15 2 19 22 9
> 5 4 2 15 9
> 5 4 2 19 9
> 6 4 2 15 9
> 6 4 2 19 9
> 12 4 2 15 9
> 12 4 2 19 9
> 2 4 5 7 9
> 2 4 5 8 9
> 6 4 5 7 9
> 6 4 5 8 9
> 2 4 12 13 9
> 2 4 12 14 9
> 5 4 12 13 9
> 5 4 12 14 9
> 6 4 12 13 9
> 6 4 12 14 9
> 7 5 4 12 9
> 8 5 4 12 9
> 4 5 8 9 9
> 4 5 8 10 9
> 4 5 8 11 9
> 7 5 8 9 9
> 7 5 8 10 9
> 7 5 8 11 9
> 4 12 1 23 9
> 13 12 1 23 9
> 14 12 1 23 9
> 1 12 4 2 9
> 1 12 4 5 9
> 1 12 4 6 9
> 16 15 2 19 9
> 17 15 2 19 9
> 18 15 2 19 9
> 1 23 24 27 9
> 1 23 24 28 9
> 25 23 24 27 9
> 25 23 24 28 9
> 26 23 24 27 9
> 26 23 24 28 9
> 23 24 28 29 9
> 27 24 28 29 9
>
> [ dihedrals ]
> ; ai aj ak al funct q0 cq
> 5 8 4 7 2
> 24 23 27 28 2
>
--
==================================================
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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