Bracht,
Amber12 divides a single POPC molecule into PA, PC, and OL parts. Using
tleap or xleap you can manually "connect" the carbon tails or heads as per
your requirement.
mani
On Tue, Apr 16, 2013 at 4:17 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> I have used the charmmgui server in order to obtain the starting structure
> for a simulation. I ran the resulting pdb through charmmlipid2amber.x but
> when I load this into tleap (already with lipid11 and ff12SB sourced) I
> get:
>
> Warning: name change in pdb file residue 1 ;
> this residue is split into PC and OL.
> .
> .
> .
> etc
>
>
> And at the end, I get :
>
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
>
> And the resulting coordinate file has disconnected residues. The carbon
> tails are disconnected from the polar heads and vice-versa.
>
> I have already patched amber and ambertools with the latest patches.
>
> Any suggestions?
>
> Thank you
> Fabrício Bracht
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>
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA.
>
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Received on Tue Apr 16 2013 - 15:00:02 PDT
