On 5/15/15 4:15 PM, Ta-Chou 黃大周 wrote:
Dear all, Actually, I had google for this error message, but I can't understand the answer clearly, and it seems the previous question didn't finish yet. I want to run a MD simulation with amber force field for a membrane protein. And the simulation box contains my goal membrane protein, POPC lipid and water, later will add ions. I choose the force field: amber99sb-ildn, and download the POPC.itp file from this website: http://bioinf.modares.ac.ir/software/mb/lipid_topology_files.htm In my top file, which will use in later grompp command. Top file as below: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "POPC.itp" ; Include chain topologies #include "tm_Protein.itp" #include "tm_Protein2.itp" #include "tm_Protein3.itp" #include "tm_Protein4.itp" ; Include water topology #include "amber99sb-ildn.ff/spce.itp" ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" ... After I type grompp command, it shows the error 'Atomtype NTL not found.' I found that the NTL atom-type showed in POPC.itp file. Can anybody help me to fix this problem? Or I should modify this itp file?
Apparently you have to also download their Amber/Slipid force field archive to get all the parameters for those atom types. Then you'll somehow have to combine all that into one functional force field.
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