Thank you for your informative reply, Sir, Now I understood the problem but when i was tried with another ligand (GSSG) It could be simulated. Later I found error for different ligand.
please give me the solution, what sort of force field should be applied? On 9 May 2011 21:27, ITHAYARAJA <ithayar...@gmail.com> wrote: > Dear Sir > > Greetings! > > I am following every gromacs applications based on your manuals. I now get > stuck in grompp -energy minimization step during generation of .tpr file for > my ligand and protein. the error which i found is the following, > > > Ignoring obsolete mdp entry 'title' > Ignoring obsolete mdp entry 'cpp' > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# > > WARNING 1 [file em.mdp, line unknown]: > Unknown or double left-hand 'coulomtype' in parameter file > > > checking input for internal consistency... > processing topology... > Opening library file /usr/share/gromacs/top/ > ffG43a1.itp > Opening library file /usr/share/gromacs/top/ffG43a1nb.itp > Opening library file /usr/share/gromacs/top/ffG43a1bon.itp > Opening library file /usr/share/gromacs/top/ff_dum.itp > Generated 279 of the 1225 non-bonded parameter combinations > > ------------------------------------------------------- > Program grompp, VERSION 4.0.7 > Source code file: ../../../../src/kernel/toppush.c, line: 947 > > Fatal error: > Atomtype CB not found > ------------------------------------------------------- > > Sir, I couldn't understand what did it refers to? So I kindly request you > spare your little time from your busy schedule to solve this problem. > > Thank you, Sir > > > -- > ** > Ithayaraja M, > Research Scholar, > Department of Bionformatics, > Bharathiar University, > Coimbatore 641 046, > Tamil Nadu > India > -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India
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