[gmx-users] how to let the grompp finding libraryfromworkingdirectory first.

[Dallas Warren]

For future reference, if someone has a similar problem, would be a good
idea to actually state what the issue you had was, and how you fixed it.

 

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 3:52 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding
libraryfromworkingdirectory first.

 

The HO.itp is nothing wrong with this.

I found the answer from last part of this page
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
membrane_protein/02_topology.html).
  
It's a bit trivial and I will test it later.

Thanks again for you time. 

lina

________________________________

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
behalf of Dallas Warren [Dallas.Warren at monash.edu]
Sent: Tuesday, September 14, 2010 1:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.

What is the contents of the HO.itp 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 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.

 

Yes.  

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina

________________________________

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
behalf of Dallas Warren [Dallas.Warren at monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from
workingdirectory first.

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.

 

Hi,

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,

lina

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100915/c03fa442/attachment.html>