Dear Mohammed, Thanks for your reply. The .ITP file from the PRODRG server has saved as drg.itp and added "#include "drg.itp"" line in the topology file. still getting the same error.
Where should I save the drg.itp file in the present working directory or share/top directory? Thanks, Aswathy Dept. Biotechnology Ext. 3108 ----- Original Message ----- From: [email protected] To: [email protected] Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 2 Send gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. RE: IN4 molecule type error (Mohammed Kamal) ---------------------------------------------------------------------- Message: 1 Date: Sun, 1 Feb 2009 21:11:11 +1100 From: Mohammed Kamal <[email protected]> Subject: RE: [gmx-users] IN4 molecule type error To: Gromacs <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" You have to include the .itp file that you have obtained from PRODRG in the topology file. Be sure that you have changed the extension of the .itp file that you have obtained from the PRODRG server from .ITP to .itp!! Mohammed > Date: Fri, 30 Jan 2009 20:57:28 +0530 > From: [email protected] > To: [email protected] > Subject: [gmx-users] IN4 molecule type error > > Dear Gromacs users, > > I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial > for a test run and i have ended up with following error. Please try to help me > > > creating statusfile for 1 node... > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# > checking input for internal consistency... > calling /usr/bin/cpp... > TEST1/trp.top:12:9: error: #include expects "FILENAME" or <FILENAME> > cpp exit code: 256 > Tried to execute: '/usr/bin/cpp -I/usr/local/gromacs/share/top -DFLEXIBLE > TEST1/trp.top > gromppVEFM2b' > The '/usr/bin/cpp' command is defined in the .mdp file > processing topology... > Generated 1284 of the 1485 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein_A 1 > Cleaning up temporary file gromppVEFM2b > Fatal error: No such moleculetype IN4 > > Can you please tell me what could be the reason for this? Please help me. > > Thanks in advance, > > Aswathy > Amrita School of Biotechnology > Dept. Biotechnology > Ext. 3108 > _______________________________________________ > 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 _________________________________________________________________ Get rid of those unwanted christmas presents! Get what you want at ebay. http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/800342b2/attachment-0001.html ------------------------------ _______________________________________________ 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! End of gmx-users Digest, Vol 58, Issue 2 **************************************** _______________________________________________ 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
