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Lipid topology for backmapping
- humiro
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8 years 1 month ago #5399
by humiro
Lipid topology for backmapping was created by humiro
Dear all,
I am using Backward to convert membrane protein from CG to AT. Atomic topology of lipids (popc.itp, dppc.itp, pope.itp,..) are required by initram.sh. I took some topoloies from Charmm-gui but it dose not work with Backward. Please tell me where can I get the topologies that are suitable for CG mapping (for charmm36 and gromos54a7).
Thank you.
I am using Backward to convert membrane protein from CG to AT. Atomic topology of lipids (popc.itp, dppc.itp, pope.itp,..) are required by initram.sh. I took some topoloies from Charmm-gui but it dose not work with Backward. Please tell me where can I get the topologies that are suitable for CG mapping (for charmm36 and gromos54a7).
Thank you.
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- tsjerk
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8 years 1 month ago #5419
by tsjerk
Replied by tsjerk on topic Lipid topology for backmapping
Hi,
The topologies from the Charmm-GUI should work, but maybe some lipids do not have a .map file yet in the Mapping directory. For most lipids it is easy enough to make mappings based on the available ones. If you make new ones, please send them to us to check and the include them in the distribution. If it doesn't work out for you, contact us and we can maybe collaborate on making them.
Best,
Tsjerk
The topologies from the Charmm-GUI should work, but maybe some lipids do not have a .map file yet in the Mapping directory. For most lipids it is easy enough to make mappings based on the available ones. If you make new ones, please send them to us to check and the include them in the distribution. If it doesn't work out for you, contact us and we can maybe collaborate on making them.
Best,
Tsjerk
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