[gmx-users] (no subject) (Soham Sarkar)

ABEL Stephane Stephane.ABEL at cea.fr
Fri Apr 5 11:55:39 CEST 2019


Hi 

In your itp you have a "?" 

?; GENERATED BY LigParGen Server

Remove it and the problem will be solved 

PS : next time add a title in you message. 

Good luck 

-
----------------------------------------------------------------------

Message: 1
Date: Fri, 5 Apr 2019 14:26:00 +0530
From: Soham Sarkar <soham9038 at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] (no subject)
Message-ID:
        <CA+fBedfs1GAY1d5K-zVDV9fGmzXFENf-iA-MWeTrUUqbwpmihQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear all,
    I am using GROMACS-2018. I want to simulate a system which contain
Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
the GROMPP command. I have defined this residue in aminoacids.rtp.

The error is like

"NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 918407885

WARNING 1 [file tba.itp, line 1]:
  Too few gb parameters for type ?


Couldn't find topology match for atomtype ?
Aborted (core dumped)"
 I have generated the itp file for TBA from ligpargen.

My itp file is

;
?; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;

[ atomtypes ]
  opls_135    C1    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_140   H11     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H12     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H13     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_159    C2    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_135    C3    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_140   H31     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H32     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H33     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_154    O4    15.9990     0.000    A    3.12000E-01   7.11280E-01
  opls_155   H41     1.0080     0.000    A    0.00000E+00   0.00000E+00
  opls_135    C5    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_140   H51     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H52     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_140   H53     1.0080     0.000    A    2.50000E-01   1.25520E-01

[ moleculetype ]
; Name               nrexcl
TBA                   3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1   opls_135      1    TBA    C1      1    -0.304408  12.0110
     2   opls_140      1    TBA   H11      1     0.098297   1.0080
     3   opls_140      1    TBA   H12      1     0.086235   1.0080
     4   opls_140      1    TBA   H13      1     0.111410   1.0080
     5   opls_159      1    TBA    C2      1     0.247098  12.0110
     6   opls_135      1    TBA    C3      1    -0.299728  12.0110
     7   opls_140      1    TBA   H31      1     0.101177   1.0080
     8   opls_140      1    TBA   H32      1     0.110693   1.0080
     9   opls_140      1    TBA   H33      1     0.110695   1.0080
    10   opls_154      1    TBA    O4      1    -0.550587  15.9990
    11   opls_155      1    TBA   H41      1     0.297574   1.0080
    12   opls_135      1    TBA    C5      1    -0.304401  12.0110
    13   opls_140      1    TBA   H51      1     0.098298   1.0080
    14   opls_140      1    TBA   H52      1     0.086234   1.0080
    15   opls_140      1    TBA   H53      1     0.111413   1.0080
[ bonds ]
    2     1     1      0.1090 284512.000
    3     1     1      0.1090 284512.000
    4     1     1      0.1090 284512.000
    5     1     1      0.1529 224262.400
    6     5     1      0.1529 224262.400
    7     6     1      0.1090 284512.000
    8     6     1      0.1090 284512.000
    9     6     1      0.1090 284512.000
   10     5     1      0.1410 267776.000
   11    10     1      0.0945 462750.400
   12     5     1      0.1529 224262.400
   13    12     1      0.1090 284512.000
   14    12     1      0.1090 284512.000
   15    12     1      0.1090 284512.000

[ angles ]
;  ai    aj    ak funct            c0            c1
c2            c3
    2     1     3     1    107.800    276.144
    2     1     4     1    107.800    276.144
    2     1     5     1    110.700    313.800
    1     5     6     1    112.700    488.273
    5     6     7     1    110.700    313.800
    5     6     8     1    110.700    313.800
    5     6     9     1    110.700    313.800
    1     5    10     1    109.500    418.400
    5    10    11     1    108.500    460.240
    1     5    12     1    112.700    488.273
    5    12    13     1    110.700    313.800
    5    12    14     1    110.700    313.800
    5    12    15     1    110.700    313.800
    7     6     9     1    107.800    276.144
    6     5    10     1    109.500    418.400
    3     1     4     1    107.800    276.144
    4     1     5     1    110.700    313.800
    3     1     5     1    110.700    313.800
   10     5    12     1    109.500    418.400
   14    12    15     1    107.800    276.144
   13    12    14     1    107.800    276.144
    7     6     8     1    107.800    276.144
    6     5    12     1    112.700    488.273
   13    12    15     1    107.800    276.144
    8     6     9     1    107.800    276.144

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    6    5    1    2        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    6    8        3       0.628   1.883   0.000  -2.510  -0.000
0.000
    6    5    1    4        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    1    2        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    1    4        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    1    3        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    6    9        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5    6    7        3       0.628   1.883   0.000  -2.510  -0.000
0.000
    6    5    1    3        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   12    5   10   11        3      -0.444   3.833   0.728  -4.117  -0.000
0.000
   15   12    5    6        3       0.628   1.883   0.000  -2.510  -0.000
0.000
    9    6    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
    8    6    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   13   12    5    6        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   14   12    5    6        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   15   12    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   13   12    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
    7    6    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   14   12    5    1        3       0.628   1.883   0.000  -2.510  -0.000
0.000
   13   12    5   10        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   15   12    5   10        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   14   12    5   10        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   11   10    5    1        3      -0.444   3.833   0.728  -4.117  -0.000
0.000
   11   10    5    6        3      -0.444   3.833   0.728  -4.117  -0.000
0.000
   10    5    6    7        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   10    5    1    4        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   10    5    1    2        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   10    5    1    3        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   10    5    6    8        3       0.979   2.937   0.000  -3.916  -0.000
0.000
   10    5    6    9        3       0.979   2.937   0.000  -3.916  -0.000
0.000

[ pairs ]
     2     6    1
     1     7    1
     3     6    1
     1     8    1
     4     6    1
     1     9    1
     2    10    1
     1    11    1
     3    10    1
     4    10    1
     2    12    1
     1    13    1
     3    12    1
     1    14    1
     4    12    1
     1    15    1
     7    10    1
     6    11    1
     8    10    1
     9    10    1
     7    12    1
     6    13    1
     8    12    1
     6    14    1
     9    12    1
     6    15    1
    11    12    1
    10    13    1
    10    14    1
    10    15    1
Please tell me where the problem is?
Thanks,
Soham



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