I am trying to simulate dppc lipid bilayer using OPLSAA forcefield. I downloaded 128-dppc.pdb, 128-dppc.top, dppc-opls.itp and opls-ua-lipid atomtypes.itp (contains only atom types) files from lipidbook.bioch.ox.ac.uk site. I copied atomtypes from the above lipid.itp to ffoplsaanb.itp. I am getting error msg: Atomtype opls_4031 not found while uisng grompp. This atom is present in lipid.itp and nonbonded.itp files.
I also looked at the link: http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-September/023761.html given in Justin's tutorial but the changes are done in the files which have parameters compatible with gromos53a6 forcefield.
Could anyone help me out with this?
I think you have to change your topology file, just add opls_4031 to the topology and define values of sigma and epsilon. I did it for tetrahydrofuran molecule, find attached.
Dear Razzakov,
Thanks for the attachment. I tried adding opls_4031 but still the same error msg comes.
hi Deepali, you could download this DPPC.itp for opls http://www.dsimb.inserm.fr/~luca/downloads/
download also the lipid_se_OPLSAA_Berger_corrected.itp in order to add the residues in the force field
and in this tutorial explains how to add the info of .itp file in gromacs
Hope it works
i forgot to put the tutorial, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
Andres
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