Gromacs simulation not running in NAMD

From: abhijit ramachandran (
Date: Mon Mar 23 2009 - 21:19:32 CDT

Hi all, I was trying to run a gromacs simulation on namd but did not succeed to get it working, i have seen many unanswered previous questions, like this one, was hoping someone answers this, has anyone run a simulation which runs in gromacs and then run in NAMD and obtained the same results. I get the following error Syntax error <0 args> in ANGELS: #include "DNA.itp" Below is file, which i had mentioned in my run file as grotopfile. This simulation is working in gromacs, but i wanted to confirm the results in NAMD but not able to run it here, any suggestions welcome. I tried removing the include statement mentioned here and copy pasted the .itp file into this .top file, then the error changed and the error was MOLECULE DNA is UNDEFINED   Is the error, since the # is used for statements that are to be discarded in NAMD scripts, but # is used with 'include' to get the header files, so I have no idea why its giving this error.    This is the .top file #include "DNA.itp"   [ system ] ; name MODEL CYLINDER [ molecules ] ; name  number DNA 1 NA  19 CL  19 W   5   This is my config file:   gromacs on grotopfile grocoorfile dna.gro numsteps   10000 outputName   eq0 XSTfile   eq0.xst minimization  on temperature  0 cellBasisVector1  33.0 0.0 0.0 cellBasisVector2  0.0 33.0 0.0 cellBasisVector3  0.0 0.0 33.0 cellOrigin  0.0 0.0 0.0 switching  on switchDist  10 cutoff   12 pairlistdist  14 margin   3 binaryOutput  yes binaryRestart  yes paraTypeCharmm  on wrapAll   yes wrapNearest  yes COMmotion  no outputEnergies  100 outputTiming  100 xstFreq   100 dcdFreq   100 restartFreq  100 timestep  0.5 nonBondedFreq  2 fullElectFrequency 4 stepsPerCycle  20 Pme   on PmeGridSizeX  48 PmeGridSizeY   48 PmeGridSizeZ  48 exclude   scaled1-4 1-4scaling  1 Thanks in advance Regards, Abhijit Connect with friends all over the world. Get Yahoo! India Messenger at

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