Re: [AMBER] lipid membrane tleap problem amber16

From: Dickson, Callum J <>
Date: Tue, 17 Jan 2017 14:29:45 +0000

Hi Sofia,

Was the format of the POPC membrane PDB exactly the same as that output from

The residue numbering should be:

PA 1

PC 1

OL 1


PA 2

PC 2

OL 2



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


PA 4

PC 5

OL 6



If this is not the case perhaps you could send your POPC membrane PDB (or a small part of it) to help diagnose further.



From: Sofia Vasilakaki <>
Sent: Monday, January 16, 2017 3:32:21 PM
Subject: [AMBER] lipid membrane tleap problem amber16


I used CHARMM-GUI to build a POPC membrane. Subsequently, I used 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

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.

AMBER mailing list
AMBER mailing list
Received on Tue Jan 17 2017 - 06:30:05 PST
Custom Search