[gmx-users] how to let the grompp finding library from workingdirectory first.

Dallas Warren Dallas.Warren at monash.edu
Tue Sep 14 06:48:39 CEST 2010

What is the contents of your topol.top and HO.itp file?  Does the
topol.top "include" the HO.itp in it?


To have an "included topology file" (.itp) file processed by grompp, it
has to be directed to it.  This is typically done by using a #include
"HO.itp" line within the topol.top file.


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from
workingdirectory first.



The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr

checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found

Do I need add something in minim.mdp? Or maybe just some parts wrong I
do not realise.

Thanks and best regards,


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