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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 16 2013 - 14:30:02 PDT
