Hi ROss:
I do use this script for CHARMM GUI direct output and there are the
same problem. I also tried the Gromacs output.
However, both CHARMM GUI and Gromacs output based input file works file
if we isolate the membrane into a individual file. The only singe
requires is simple keep the lipids in right name such as POPE and so on.
I found a issue for this: the output for this script don't contains a
full name for POPE it will split a lipids into PA, PE, POPE in the
output file.... I am not sure whether it is correct for such cases.
When I load with tleap, it also have some warnings: XXX name changed.....
thank you very much
Albert
On 05/08/2012 06:46 PM, Ross Walker wrote:
> Hi Albert,
>
> The charmmlipid2amber.x script expects very specific input. It is not
> designed to be bullet proof. It expects output from the Charmm lipid
> builder. If your pdb is not in that specific format then you will have to
> manually convert it. How specifically did you get your initial lipid pdb
> file?
>
> Ben can answer more when he gets in but I also suspect, although I haven't
> looked at the script in a while, that it is not designed to work with pdbs
> containing protein and waters. You will need to remove these from the file,
> run the script to convert the lipid naming and then manually put the water
> and protein back in. These are pretty advanced calculations so you will need
> to do a lot of the leg work yourself I'm afraid. It will be quite a while
> until everything can be properly automated I'm afraid.
>
> All the best
> Ross
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Received on Tue May 08 2012 - 10:30:04 PDT
