Hi Amber User,
I’m trying to simulate a membrane system and I tried to make the lipid via tleap.
>>source leaprc.protein.ff14SB
>>source leaprc.lipid17
>>lipid = sequence {MY PC MY}
>>savepdb lipid lipid.pdb
However, I notice that instead of having a ter at the end of the molecule, there is a ter at the end of the first acryl chain (MY) another ter at the end of the head group (PC) and a final ter at the end of the molecular.
I felt that there shouldn't be a ter at the end of the first acryl chain and the head group. If I load this tleap made pdb back to tleap to generate the topology.
>>source leaprc.protein.ff14SB
>>source leaprc.lipid17
>>lipid = loadpdb lipid.pdb
>>saveamberparm lipid MM.prmtop MM.inpcrd
The head group will leave the lipid during the simulation.
Kind regards,
Zhiyi Wu
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Received on Mon Jun 08 2020 - 03:00:02 PDT
