Hi Fabricio,
Are all of the atom types being assigned correctly when you're loading into LEaP? I'm wondering if the topology is not being read correctly by LEaP for your input PDB.
Can you verify that your PDB file is formatted as follows for the lipids?
sn-1 tail residue
head group residue
sn-2 tail residue
TER card
sn-1 tail residue
head group residue
sn-2 tail residue
TER card
...
When you execute 'saveAmberParm' does LEaP display any errors about missing parameters? Does your resulting prmtop and inpcrd file have the correct connections?
If that all seems normal, can you send me your input file off the list, and I can take a look to see what's happening in LEaP.
All the best,
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: Fabrício Bracht [bracht.iq.ufrj.br]
Sent: Wednesday, April 17, 2013 10:40 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
But this must be something that was changed in one of the bug fixes,
because I processed a membrane file a few months ago and got the correct
structure after going through tleap.
2013/4/17 manikanthan bhavaraju <mhb75.msstate.edu>
> I had to face the same problem. I tired changing the charmmlipid2amber.x
> script for POPC to obtain proper bond ordering. Finally, I have manually
> connected the carbon (tail/head) using "connect" command. I have not seen
> anyone commenting on this issue in the amber mailing list.
>
>
> mani
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Received on Wed Apr 17 2013 - 17:00:03 PDT
