[AMBER] lipids14 pdb format

From: Sergio Decherchi <Sergio.Decherchi.iit.it>
Date: Fri, 19 Sep 2014 11:31:45 +0000

Dear AmberTools Users/Developers,
I would like to know some information about the PDB format for lipid14.
I followed the very nice tutorial at:


If I am not wrong, the format says that every lipid has a unique residue
number but inside that residue the names of the residues change (tails,head).
Is this correct?

I tried the following with tleap:

- usual preload of libs
- load such formatted pdb on tleap
- save the pdb, call it test.pdb
- save the topology, call it a.prmtop

Then again tleap;
- usual preload of libs
- load test.pdb in tleap
- save the topology, call it b.prmtop

I checked a.prmtop and it is different from b.prmtop. Why they are different?
The suggested PDB format for the lipids is strictly necessary to get a correct topology?
If this is the case, tleap does not complain when saving b.prmtop; which is the
meaning of this topology?

Thanks a lot!

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Received on Fri Sep 19 2014 - 05:00:02 PDT
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