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 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of nitu sharma Sent: Friday, 24 April 2009 2:40 PM To: [email protected] 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????????????????????? _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
