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

[Justin A. Lemkul]

Stephane Abel wrote:
> 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 ?
> 

I would echo what Mark has said - the only clean way to make this work is to use 
a compatible version of Gromacs (4.5.3 preferably).  There have been significant 
changes between 4.0.7 and 4.5, and anything you might hack to "make work" would 
be questionable.

-Justin

> 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
>>>
>>>
>>>
>>>     
>>
>>   
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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