Dear, Gromac's users!
Today I've tried to make pure lipid bi-layer system from initial .pdb structure with the parametrization by the charmm ff. The main goal of this step is preparing the initial structure suitable for the futher simulation ( creating gro, top and posre files) First I've download s system consisted of 72 dppc lipids solved with water. Then I've succesfull created .gro as well as .top files by the pdb2grmx for my lipid system. But on futher during creatinon of the tpr file by gromp I've obtained many errors like this ERROR 4378 [file topol.top, line 83773]: No default U-B types Also I've tried to make my own bi-layer by VMD membrane plugin. After processing of this file by pdb2gmx I've obtained many .itp files like topol_Other_chain_L2.itp included in the generated topology file topol.top. But during loading this structure to the grompp I've obtained above mentioned error again. In both cases I've used mdp file for gromp consist of minimization algorithm ( attached). What I've done wrong? Could you provide me with the workable algorithm for preparation of the pure lipid system parametriezed by charm27 ? Finally I have small queation about charmm structures- I've found already pre-equilibrated bi-layers http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb file is accompanied by the PSF ones. As I've understood the PSF is the same to the top in the Gromacs. Could I convert PSF to the TOP for already pre-built system? Thanks for help James James
topol.top
Description: Binary data
minim.mdp
Description: application/mdp
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