Hi Ben. The input pdb for tleap has that exact order. All atom types are
being assigned correctly, I mean, there are no warnings or errors except
the warnings about :
name change in pdb file residue 1 ;
this residue is split into PC and OL
Saveamberparm does not display any errors either and the resulting prmtop
show no linkage between the tails and the head residues. All other
connections seem to be correct.
I'll send the files to your email.
Thanks
Fabrício Bracht
2013/4/17 Benjamin D Madej <bmadej.ucsd.edu>
> 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 Thu Apr 18 2013 - 11:30:02 PDT
