[gmx-users] adding ETHANOL to CGennFF in gromacs has problem
Justin Lemkul
jalemkul at vt.edu
Mon Sep 2 19:34:39 CEST 2013
Please make sure to keep the discussion on the mailing list.
On 9/2/13 1:27 PM, Golshan Hejazi wrote:
> This is the gro file that I am using:
> ETHANOL
> 9
> 1ETHA C1 1 3.133 3.266 0.008
> 1ETHA O1 2 3.244 3.350 -0.021
> 1ETHA HO1 3 3.324 3.296 -0.015
> 1ETHA H11 4 3.143 3.225 0.111
> 1ETHA H12 5 3.129 3.182 -0.065
> 1ETHA C2 6 3.007 3.351 -0.002
> 1ETHA H21 7 3.011 3.435 0.071
> 1ETHA H22 8 2.998 3.394 -0.104
> 1ETHA H23 9 2.917 3.290 0.019
> 3.41840 3.44350 3.38360
>
> This is what I added in the rtp:
>
> [ ETHA ]
> [ atoms ]
> C1 CG321 0.05 0
> O1 OG311 -0.65 1
> HO1 HGP1 0.42 2
> H11 HGA2 0.09 3
> H12 HGA2 0.09 4
> C2 CG331 -0.27 5
> H21 HGA3 0.09 6
> H22 HGA3 0.09 7
> H23 HGA3 0.09 8
> [ bonds ]
> C1 C2
> C1 O1
> C1 H11
> C1 H12
> O1 HO1
> C2 H21
> C2 H22
> C2 H23
>
> And this is the resulting topology:
>
> ; Include forcefield parameters
> #include "./charmm36.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> drug 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> ; residue 1 ETHA rtp ETHA q 0.0
> 1 CG321 1 ETHA C1 1 0.05 12.011 ; qtot 0.05
> 2 OG311 1 ETHA O1 2 -0.65 15.9994 ; qtot -0.6
> 3 HGP1 1 ETHA HO1 3 0.42 1.008 ; qtot -0.18
> 4 HGA2 1 ETHA H11 4 0.09 1.008 ; qtot -0.09
> 5 HGA2 1 ETHA H12 5 0.09 1.008 ; qtot 0
> 6 CG331 1 ETHA C2 6 -0.27 12.011 ; qtot -0.27
> 7 HGA3 1 ETHA H21 7 0.09 1.008 ; qtot -0.18
> 8 HGA3 1 ETHA H22 8 0.09 1.008 ; qtot -0.09
> 9 HGA3 1 ETHA H23 9 0.09 1.008 ; qtot 0
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 4 1
> 1 5 1
> 1 6 1
> 2 3 1
> 6 7 1
> 6 8 1
> 6 9 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 2 7 1
> 2 8 1
> 2 9 1
> 3 4 1
> 3 5 1
> 3 6 1
> 4 7 1
> 4 8 1
> 4 9 1
> 5 7 1
> 5 8 1
> 5 9 1
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 4 5
> 2 1 5 5
> 2 1 6 5
> 4 1 5 5
> 4 1 6 5
> 5 1 6 5
> 1 2 3 5
> 1 6 7 5
> 1 6 8 5
> 1 6 9 5
> 7 6 8 5
> 7 6 9 5
> 8 6 9 5
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 4 1 2 3 9
> 5 1 2 3 9
> 6 1 2 3 9
> 2 1 6 7 9
> 2 1 6 8 9
> 2 1 6 9 9
> 4 1 6 7 9
> 4 1 6 8 9
> 4 1 6 9 9
> 5 1 6 7 9
> 5 1 6 8 9
> 5 1 6 9 9
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> [ system ]
> ; Name
> ETHANOL
>
> [ molecules ]
> ; Compound #mols
> drug 1
>
All of this looks perfectly normal. What are you trying to do when it flies
apart? Are you dealing with a single molecule only?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
More information about the gromacs.org_gmx-users
mailing list