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On 9/02/2011 11:07 PM, shiva birgani wrote:
<blockquote
cite="mid:AANLkTim3UuiJUZggWbdTwdxOd_apvF2m36xGooeznCP-@mail.gmail.com"
type="cite">Dear Justin<br>
I fallowed your tutorial of "<font size="1"><font><font
face="Arial">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<br>
<br>
WARNING 1 [file nvt.mdp, line unknown]:<br>
Unknown left-hand 'continuation' in parameter file<br>
<br>
checking input for internal consistency...<br>
calling cpp...<br>
processing topology...<br>
Generated 279 of the 1225 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for Protein_A 1<br>
turning all bonds into constraints...<br>
Excluding 3 bonded neighbours for ACY 1<br>
turning all bonds into constraints...<br>
Excluding 2 bonded neighbours for SOL 6648<br>
turning all bonds into constraints...<br>
Excluding 1 bonded neighbours for NA+ 1<br>
turning all bonds into constraints...<br>
Excluding 1 bonded neighbours for CL- 0<br>
turning all bonds into constraints...<br>
NOTE:<br>
System has non-zero total charge: -9.999999e-01<br>
<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
WARNING 2 [file "topol.top", line 1453]:<br>
For energy conservation with LINCS, lincs_iter should be 2
or larger.<br>
You can safely ignore this if your system doesn't have any<br>
LINCS-constrained bonds;<br>
for water molecules we normally use the analytical SETTLE
algorithm<br>
instead.<br>
Setting gen_seed to 261405<br>
Velocities were taken from a Maxwell distribution at 300 K<br>
<br>
There were 2 warnings<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.3<br>
Source code file: grompp.c, line: 1132<br>
<br>
Fatal error:<br>
There were 1 error(s) processing your input<br>
-------------------------------------------------------<br>
<br>
how should I do correct it?<br>
</font></font></font></blockquote>
<br>
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.<br>
<br>
Mark<br>
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