On 18/02/2012 7:50 PM, xiaojiong wrote:
Dear,
My receptor is membrane proteins,then I get protein-ligand complex.I
want to do MD simulations in DPPC.I use the GROMOS96 53a6 force
field modified in order to include Berger’s parameters for lipids .The
topology for the ligand was created
employing the server PRODRG 2.5 Beta.
When I finished the command "perl inflategro.pl system.gro 4 DPPC 14
system_inflated.gro 5 area.dat",
I want to run energy minimization.I submit the command "grompp -f
minim.mdp -c system_inflated.gro -p topol.top -o em.tpr".The error
like this
Back Off!Ijust backed up mdout.mdp to ./#mdout.mdp.4#
Generated 813 of the 2346 non-bonded parameter combinations
WARING 1 [file drg.itp,line1]:
Too few parameters on line (source file toppush.c, line 1501)
WARING 2 [file drg.itp,line2]:
Too few parameters on line (source file toppush.c, line 1501)
WARING 3 [file drg.itp,line17]:
Too few parameters on line (source file toppush.c, line 1501)
ERROR 1 [file drg.itp,line 21]:
Expected a molecule type name and nrexcl
Apparently you are not following the correct file format. You'll have to
consult chapter 5 of the manual and look at these lines and see what
might be wrong.
Program grompp, VERSION 4.5.3
Source code file:toppush.c, line:1187
Fatal error:
Atomtype \par not found
Is the force field not suitable or others?Thanks!
The formatting is wrong, but we can't tell how.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
