[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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