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? thanks in advance Shiva
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