[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

==================================================



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