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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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
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