dear all,
also, please consider ben's previously e-mails concerning the format of the
PDB to be read with lipid11 -->
http://archive.ambermd.org/201205/0352.html
best regards,
igor
Igor Marques, *Researcher*
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences
Molecular Modeling Group – University of Aveiro
http://molecular-modeling.dq.ua.pt/
Mobile phone: +351 918 567 294
Phone: +351 234 370 200 Ext: 22102
Campus Universitario de Santiago
Edificio III
3810-193 Aveiro
Portugal
On Thu, Apr 18, 2013 at 12:48 AM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> 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 - 07:00:02 PDT
