Hi Ben:
thanks a lot for reply.
Yes, I use the attached new script for converting. and I found that
the output for Groamcs editconf and CHARMM GUI output is different. The
CHARMM GUI output is the same as you mentioned while the Gromacs
editconf output is different. the POPE from editconf contains:
PA,PC,OL,POPE
when I load into tleap and source liaprc.lipid11, I got warning:
this residue is split into PA 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 PA and PC.
Warning: name change in pdb file residue 2 ;
this residue is split into PC and OL.
thank you very much
best
Albert
On 05/08/2012 09:10 PM, Benjamin D Madej wrote:
> Albert,
>
> Did you try the latest script that I posted in the last email?
>
> POPC should have three residues: PA, PC, and OL in that order.
> POPE should have three residues as well: PA, PE, OL.
>
> A PDB from CHARMM-GUI with those residues can be loaded ('loadpdb' command) into LEaP after you have loaded your force field (for example, 'source leaprc.lipid11').
>
> Best,
> Ben Madej
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Received on Tue May 08 2012 - 12:30:03 PDT
