[gmx-users] Use an altenative folder for itp files

[Stephane Abel]

OK thank you for your help justin

With the change you have suggested, grompp starts but an other error 
come quickly with the first line of the gb.itp:

ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]:
Invalid directive implicit_genborn_params


-------------------------------------------------------
Program grompp_mpi, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.155
-------------------------------------------------------

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)

Here the head of my gb.itp file

[ implicit_genborn_params ]
; Atom type sar st pi gbr hct

NH1 0.155 1 1.028 0.17063 0.79 ; N

I have tried to pass this error by commenting the #include "gb.itp" 
statements in the forcefield.itp file with no success.

Do you have any other (good) suggestion ?

Stefane




>
> ------------------------------
>
> Message: 3
> Date: Wed, 17 Nov 2010 07:59:20 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files]
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CE3D1A8.9070003 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Stephane Abel wrote:
>   
>> Dear all,
>>
>>
>> I have a little question about the use of a alternative localization of 
>> the ff librairy in GMX4.0.7. These (old) version of GMX is installed in 
>> a big cluster and i would like to use it for testing some CHARMM27 
>> parameters. Since the charmm27.ff is not given this distribution, i 
>> would like to use my own ff lib, so i have placed my home directory the 
>> charmm27.ff directory with all the necessary files. As expected, when i 
>> use grompp, i have an error :
>>
>>
>> Fatal error:
>> Library file ffnonbonded.itp not found in current dir nor in default 
>> directories.
>> (You can set the directories to search with the GMXLIB path variable)
>>
>>
>> How to indicate to grompp that the charmm27.ff is my directory say 
>> /home/cont003/stefane/charmm27.ff/
>>
>>
>> I have read that the include directive can do the job, so i placed the 
>> path of the charmm27.ff like this in my mdp file
>>
>>
>> include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp
>>
>>
>> but the program hangs:
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
>> checking input for internal consistency...
>> processing topology...
>>
>>
>> have I missed something ?
>>
>>     
>
> The "include" keyword should point to a directory in which your .itp files 
> reside, not an .itp file itself.
>
> -Justin
>
>   
>> Thanks in advance for your help
>>
>>
>> Stefane
>>
>>
>>
>>     
>
>