[gmx-users] Force field parameters not known

Peter Stern peter.stern at weizmann.ac.il
Sat Feb 23 13:17:02 CET 2019


It seems that you typed "cp-r" (no space) instead of "cp -r" (space between cp and -r).
"cp" is a Linux command, not Gromacs and as such, anything that starts with a "-" is part of a flag or option to the command.
There may be several such flags and they are space delimited.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Matthew Stoodley
Sent: Thursday, February 21, 2019 12:59 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Force field parameters not known

I am currently trying to perform a simulation on a chemical molecular machine but whenever I try and do the pdb2gmx command and select a force field it comes up with the message 'the residue DVHY is not recognised'. From my understanding what I should do is to update the residue in the specific force field that I want to use. I have tried using the command line: 

cp-r $GMXLIB/residuetypes.dat  $GMXLIB/amber99sb.ff

as it says to use this on the gromacs website but it says the command is not recognised. I am using GROMACS 5.0.4.
Any help would be appreciated.Thanks,Matthew
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