Hi Sofia,
Was the format of the POPC membrane PDB exactly the same as that output from charmmlipid2amber.py?
The residue numbering should be:
PA 1
PC 1
OL 1
TER
PA 2
PC 2
OL 2
TER
....
Each POPC lipid has PA, PC and OL units with each single lipid having the same residue number. That you do not see a bond between tails and head groups indicates your membrane PDB has residue numbering as:
PA 1
PC 2
OL 3
TER
PA 4
PC 5
OL 6
TER
....
If this is not the case perhaps you could send your POPC membrane PDB (or a small part of it) to help diagnose further.
Best,
Callum
________________________________
From: Sofia Vasilakaki <svasilak.chem.uoa.gr>
Sent: Monday, January 16, 2017 3:32:21 PM
To: amber.ambermd.org
Subject: [AMBER] lipid membrane tleap problem amber16
Hi,
I used CHARMM-GUI to build a POPC membrane. Subsequently, I used
charmmlipid2amber.py and then I loaded the pdb file in tleap, after
leaprc.water.tip3p, leaprc.lipid14, leaprc.protein.ff14SBonlysc and
finally leaprc.gaff2. (My system includes a protein and an inhibitor as
well.)
The bond between the head and the tail groups of the lipids does not
appear when I open the prmtop/inpcrd files in VMD. I have tried a couple
of things I found by google it but ... no luck.
It would be nice if you could suggest a workaround to this.
Thank you in advance!
Kind Regards,
Sofia V.
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Received on Tue Jan 17 2017 - 06:30:05 PST
