On 9/02/2011 11:07 PM, shiva birgani wrote:
Dear Justin
I fallowed your tutorial of "Protein-Ligand Complex" to simulate a
peptide associated with acetic acid. All the step was good but in
Equilibration phase 1 I encountered with this error
WARNING 1 [file nvt.mdp, line unknown]:
Unknown left-hand 'continuation' in parameter file
checking input for internal consistency...
calling cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for ACY 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6648
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 1
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 0
turning all bonds into constraints...
NOTE:
System has non-zero total charge: -9.999999e-01
processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 1453]:
For energy conservation with LINCS, lincs_iter should be 2 or larger.
You can safely ignore this if your system doesn't have any
LINCS-constrained bonds;
for water molecules we normally use the analytical SETTLE algorithm
instead.
Setting gen_seed to 261405
Velocities were taken from a Maxwell distribution at 300 K
There were 2 warnings
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1132
Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------
how should I do correct it?
You're probably using a version of GROMACS that is years older than the
tutorial, and so will have minor compatibility issues. More recent
versions offer much better performance.
Mark
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