Hello,
I'm try to load my pdb file in to amber using xleap command:
>memS1 = loadPdb DOPC_128_lipid12cp.pdb
however, it seems something is going wrong, because it keeps showing:
>Warning: name change in pdb file residue 1;
> this residue is split into OL and PC.
>Warning: name change in pdb file residue 1;
> this residue is split into PC and OL.
>Warning: name change in pdb file residue 2;
> this residue is split into OL and PC.
>Warning: name change in pdb file residue 2;
> this residue is split into PC and OL.
....
(and it keeps showing all the 286 residue is split to OL and PC, PC and OL.)
>Created a new atom named: HT1 within residue: .R<NASN 1>
>Created a new atom named: HT2 within residue: .R<NASN 1>
...
(and it keeps showing all the 22 amino acid name has been created.)
If I ignore these warnings and keep going to generate *.prmtop and *.inpcrd file, it just doesn't work, with warning me (for example):
> Faltal: Atom .R<NASN 1>. does not have a type.
I have tried to uss addPdbAtomMap to map the changing names, it's still useless. So could you please tell me how to solve these problems?
Thanks a lot!
Sincerely yours,
Helen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 16 2013 - 13:30:02 PST
