[gmx-users] Shima Arasteh wants to share a link | Gromacs

Emanuel Birru Emanuel.Birru at monash.edu
Thu Mar 29 08:56:31 CEST 2012

Check your topology file. The atom LC3 is not found in Gromacs .atp file. 

How did you generate your .top file? If you generate it using pdb2gmx it should not give you such error.


Emmanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.birru at monash.edu 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of rossen at kth.se
Sent: Thursday, 29 March 2012 4:53 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Shima Arasteh wants to a share a link on the Gromacs wiki: http://www.gromacs.org/

Shima Arasteh says:
Dear Gromacs friends,
I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction but I face a fatal error when I enter this command:
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

And the fatal error is this:
atomtype LC3 not found

Anybody can suggest me a solution to solve my problem?

Thanks in advance
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