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>thanks in advance <br>Shiva<br></font></font></font>