On Tue, Jan 27, 2015 at 8:38 AM, Romero, Raquel <raquel.romero.12.ucl.ac.uk>
wrote:
> Dear all,
>
> Thanks a lot for your replies, I will now explain the protocol I followed
> in order you to completely understand my problem:
> ( For a 300 DPPC lipid membrane with no proteins):
>
> 1. Converting the pre-equilibrated, solvated and neutralised DPPC membrane
> using the script charmmlipid2amber and the reference table
> charmmlipid2amber.csv (after this steps the each lipid is a single residue
> with a TER card after each one).
>
> 2. Obtaining box dimensions using the script vmd_box_dims.sh.
>
> 3. Loading the system into tleap in order to obtain amber parameters.
> Setting box dimensions using the values obtained in the step above. ( After
> saving pdb in this step it is observed that each lipid got divided into 3
> residues with a TER card after each one, however it seems to have bonds
> between residues.)
>
​After this step, take the prmtop and run the "checkValidity" action in
ParmEd on it. For example:
parmed.py -p lipid.prmtop -c lipid.inpcrd
> checkValidity
This will run certain checks and spit out warnings if any problems were
detected. tleap has known issues with respect to molecule detection in
complex cases, which has resulted in some strange issues in the past. I'm
not certain that this is the problem, but if it is, ParmEd will check (and
tell you how to fix) it.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 27 2015 - 08:00:04 PST
