Dear RG users,
I am writing for some assistance in generating a lipid bilayer membrane as per the user need.
The present lipid databases contains generally 128/64 lipids or bigger.
I would like to use a small system comprised of 40 lipids.
I tried to replicate one system using gromacs genconf command (Protocols- Downloaded DPPC128 from lipid database; selected residue 1 to 2 in VMD and saved without water, using genconf tried to replicate with nbox 20 1 1).
However, the system is too large as per the box coordinate size is concern. A random box size define may create technical artifact.
Thus in this regard, could somebody help me in creating such a small system using any other techniques.
Thanking you in anticipation of your reply.
Best regards,
Bikash
Dear Dr. Abel and Maroli,
Thank you for your suggestions. I am aware about the CHAMM_GUI, however, I would like to use Amber-ff. Small lipid membrane is a good target to investigate bio-transportation at multi-microsecond scale. Thus, I am trying to generate a small system for such analysis to ward off the computational inadequacy at my institution. I need a all-atom map where CG and UA at present holds ample limitations. After removing the excess lipids, defining the box size randomly may give artifacts. Thus, I am looking for the availability of other techniques.
Best regards,
Bikash
Hi bikash; I think this link might be useful....
http://bioinf.modares.ac.ir/software/mb2/builder.php
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