That does not make any sense. If tleap disconnects the parts and I haveto
manually connect them back, this means that for 300 residue membrane, I'll
have to type the bond command 600 times.
Em 16/04/2013 18:36, "manikanthan bhavaraju" <mhb75.msstate.edu> escreveu:
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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > 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 - 19:30:03 PDT
