On Fri, Dec 11, 2015 at 12:06 AM, mohammad r <mohammad.r0325.yahoo.com>
wrote:
> Hi David,
> This the commands which I used:> source leaprc.ff14SB> loadAmberParams
> frcmod.ionsjc_tip3p> mol=loadpdb solvated.pdb
> And then I tried to save parameters. CLA is Chloride.By the way, when I
> save a pdb or parameter files in tleap, it automatically add hydrogen to
> all the residues. Is there any way to make the tleap not to do that?
>
As Brian mentioned, CLA and SOD are CHARMM-specific names for chloride and
sodium ions. Amber understands different names.
What this indicates to me is that you are using the PDB you got directly
from CHARMM-GUI inside tleap to try and make your prmtop file. This isn't
going to work. You need to run charmmlipid2amber.py on your PDB file. For
instance, something like
charmmlipid2amber.py -i solvated.pdb -o solvated_amber.pdb
Then you need to use "solvated_amber.pdb" for the loadPDB command in tleap
instead of solvated.pdb. Also, if there are lipids in your system, you
need to source leaprc.lipid14 in addition to leaprc.ff14SB (if there is
also a protein). So your leap commands should look something like
source leaprc.ff14SB
source leaprc.lipid14
mol = loadpdb solvated_amber.pdb
...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 11 2015 - 04:30:03 PST
