[gmx-users] Help with grompp with amber99 forcefield

Ragnarok sdf fabracht1 at gmail.com
Tue Aug 19 19:46:18 CEST 2008


Hello, I've searched the archives in search of an answer for my problem and
was able to solve only part of the problem.
I am working with a DNA/Protein system with AMBER99 forcefield.
The first problem is
"...Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
ERROR 0 [file "1VKX_C.itp", line 420]:
  No default Bond types
ERROR 0 [file "1VKX_C.itp", line 1803]:
  No default Angle types
ERROR 0 [file "1VKX_C.itp", line 1805]:
  No default Angle types
ERROR 0 [file "1VKX_D.itp", line 418]:
  No default Bond types
ERROR 0 [file "1VKX_D.itp", line 1782]:
  No default Angle types
ERROR 0 [file "1VKX_D.itp", line 1784]:
  No default Angle types
Excluding 3 bonded neighbours for Protein_A           1
Excluding 3 bonded neighbours for Protein_B           1
Excluding 3 bonded neighbours for Protein_C           1
Excluding 3 bonded neighbours for Protein_D           1
Excluding 2 bonded neighbours for SOL             23807
NOTE:
  System has non-zero total charge: -1.214508e+02

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   9500
#     ANGLES:   16856
#      PDIHS:   1881
#     RBDIHS:   19280
#       LJ14:   23897
#     SETTLE:   23807

-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1205

Fatal error:
There were 6 errors in input file(s)
-------------------------------------------------------..."
And the second error is the total system carge which is a non integral
charge.
I've looked for  the " ERROR 0 [file "1VKX_C.itp", line 420]:
  No default Bond types" solution but no one seams to have had the same
problem as I.
I believe the charge problem can be found in the users list, so the actual
doubt lies in the first problem.
Thank you in advance
Fabrício Bracht
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