[gmx-users] Re: gmx-users Digest, Vol 79, Issue 124

[Stephane Abel]

OK thank you all, I give up  :-(

a bientot

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