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AMBER Archive (2003)Subject: RE: structure image
From: Xiang, Tian-Xiang (txian2_at_email.uky.edu)
>You might try:
>trajin <filename>.crd
>This worked for me! (using ptraj-6.2 or 6.3)
This may work if the system is not moved too far from the initial structure. It does not work for me as parts of some lipids have moved outside the central box while the rest parts of the lipids remain in the box. How ptraj can handle this?
>I am very interested, because I switched from AMBER to GROMACS (or rather
Indeed, I may not have all the right amber forcefield paramters for lipid bilayers. We used some from Charmm and developed a few our own. Someone out there may be trying to make the Charmm forcefiled for lipid bilayers compatible to amber. I would be very interested to know where the source. Amber does not provide enough tools to analyze bilayer properties. We have used ptraj and carnal to calculate some properties but have to write some codes ourselves specifically meet our own need.
T.X. Xiang
"Xiang, Tian-Xiang" wrote:
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