[gmx-users] Re: gmx-users Digest, Vol 58, Issue 2

[Mohammed Kamal]

Saving it in the working directory should work fine..... I hope that you have added the #include line in the right place within the topology file
Mohammed

> Date: Sun, 1 Feb 2009 16:49:17 +0530
> From: aswathys at amritapuri.amrita.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> 
> 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 -----
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> To: gmx-users at gromacs.org
> 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
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> 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 <mohkam978 at hotmail.com>
> Subject: RE: [gmx-users] IN4 molecule type error
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID: <BAY118-W17CC364801C129280EA54EF4C40 at phx.gbl>
> 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: aswathys at amritapuri.amrita.edu
> > To: gmx-users at gromacs.org
> > 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
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