AMBER Archive (2009)

Subject: [AMBER] lipid membrane(dppc) in amber

From: xueqin pang (pangxueqintea_at_yahoo.com.cn)
Date: Fri May 22 2009 - 04:01:26 CDT

Hello every,
   I am simulating a GPCR in membrane doundaries, using AMBER 9/10. As a greenhand of AMBER, I got several problems with the simulation after referring to some related papers as well as the manual of AMBER.
1.  If I am using. GAFF can I use the parameters of GROMOS-96 force field for dppc?
2. If not where can I get parameter and topology for dppc in Amber ( I have surf the net but field.)
3. Someone suggested that "doing NPT in AMBER with ntp=2 leads to more unrealistic membrane properties than doing NPT in NAMD with the Langevin piston method to control the pressure" (http://archive.ambermd.org/200808/0100.html). Is that true with you?
 
Thanks a lot

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