AW: Running gromacs in namd

From: Norman Geist (
Date: Wed Nov 30 2016 - 02:45:09 CST

Have you tried sending your topology through one of the gromacs tools to check it is correct? Otherwise, since gromacs support in namd is rather rudimentary, you could also try to convert your gromacs files to amber format using the Parmed tool, either directly downloaded from github or shipped with the Ambertools 16, as:



parmed> gromber your.gro

parmed> outparm your.prmtop your.rst7


It might also output errors your topology has issues. Later in namd you do;


amber on

parmfile your.prmtop

ambercoor your.rst7


Best wishes


Norman Geist


Von: Subbarao Kanchi []
Gesendet: Dienstag, 29. November 2016 11:25
An: Norman Geist <>
Betreff: Re: namd-l: Running gromacs in namd


Hi Norman Geist,

                        I have copied the *.itp into the topologies file (.top) and end up with another error "Syntax error in ATOMS" as reported in mailing list I do not find any solution to overcome the error.


Subbarao Kanchi


On Tue, Nov 29, 2016 at 1:06 PM, Norman Geist < <> > wrote:

Well, the exact error is just:


Molecule DMPC undefined


This is because namd doesn’t follow linked *.itp files from your topology file. Please just copy the content of all required *.itp files into your *.top file and try again.


Best of luck


Norman Geist

Von: <> [ <> ] Im Auftrag von Subbarao Kanchi
Gesendet: Dienstag, 29. November 2016 07:31
An: <>
Cc: <>
Betreff: namd-l: Running gromacs in namd


Dear Michael Makowski,

                                   I am trying to run gromacs simulation in namd and getting the error "USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Molecule DMPC undefined" I have seen your post in the mailing list "". Could you let me know that how did you overcome this problem to run gromacs simulation in namd.


Subbarao Kanchi.



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