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" <[email protected]>
Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files]
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
