[gmx-users] grompp error

[Dallas B. Warren]

Both of those errors are telling you want you need to do.  In your
topol_A.itp file, there are no parameters for a particular proper
dihedral.  So, define one.  Same with the next message.  And it even
tells you which line the issue is on in the .itp file, so very easy to
track down which bonds are the issue and so on.
 
I would recommend you read the errors, then check them against what is
the wiki, then search the emailing list.  Rarely does an error come up
that has not been discussed and solved before.  Many of the errors you
are encounting are nothing out of the ordinary.
 
And the non-zero charge, well being non-zero is not a real issue.  What
is the real issue is that it is a non-integer.  If it was an integer,
then that simply means you need counter ions.  But being non-integer
means you have a problem with the charges on that atoms in your
topology.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 



________________________________

	From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of nitu sharma
	Sent: Friday, 24 April 2009 2:40 PM
	To: gmx-users at gromacs.org
	Subject: [gmx-users] grompp error
	
	
	Dear MARK 
	
	                     Now the problem of matching of topology
file and coordinate file solved  but the other two errors come during
running grompp in the second step of inflategro .
	my command line is like this- grompp -f em.mdp -p
topolinflate.top -c inflated_system.gro -o inflated-em.tpr
	
	the error came is like this-
	ERROR 1 [file topol_A.itp, line 29912]:
	  No default Proper Dih. types
	
	
	ERROR 2 [file topol_B.itp, line 26604]:
	  No default Proper Dih. types
	
	Excluding 3 bonded neighbours molecule type 'Protein_A'
	Excluding 3 bonded neighbours molecule type 'Protein_B'
	Excluding 3 bonded neighbours molecule type 'DMPC'
	
	NOTE 1 [file topolinflate.top, line 33]:
	  System has non-zero total charge: -1.161999e+01
	  
	
	
	processing coordinates...
	double-checking input for internal consistency...
	renumbering atomtypes...
	converting bonded parameters...
	
	There was 1 note
	
	-------------------------------------------------------
	Program grompp, VERSION 4.0.3
	Source code file: grompp.c, line: 986
	
	Fatal error:
	There were 2 errors in input file(s)
	-------------------------------------------------------
	
	can you suggest me what is the possible way to solve this
problem and in case of note - system has non zero charge how can i make
its neutral?????????????????????