Subject: MD simulations of DPPC bilayers

From: kzong <[email-masked]>
Date: Thu, 24 Oct 2002 15:36:24 +0800

Dear all:
  I wanted to apply CHARMM to do some MD simulations of DPPC bilayers. But I ment some difficulty in building the inital conformation. I used build-seq.inp(in attachment) to setup one dppc, but it counldn't produce the atom coordinates. Then I tried to use the conformation in support directory of charmm(support/membrane/dppc.tar.gz), but the format seemed imcompatible. I also searched the web to find a pre-equilibrated conformation. I found one(dppc_feller_feb99.crd) in
http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/membrane.html
But there didn't give more information of this conformation(details of the simulation). Anyone could give me some advice?

                                                               Chen Hao

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From: Simon Berneche <[email-masked]>
Date: Thu, 24 Oct 2002 11:29:38 -0400

Chen,

Which version of CHARMM are you using? The input that you attached is  
compatible with topology files of version c29 and newer. Starting with  
CHARMM c29, the topology file for lipids splits DPPC in sub-components:  
  residues PALM and PCGL. Previous versions considered DPPC as a single  
residue.

If you want to use the files in charmm's support/membrane directory  
you'll have to use the parameter and topology files included in there,  
which basically correspond to those distributed with CHARMM c26 to c28.

Simon

> Dear all:
>   I wanted to apply CHARMM to do some MD simulations of DPPC bilayers.  
> But I ment some difficulty in building the inital conformation. I used  
> build-seq.inp(in attachment) to setup one dppc, but it counldn't  
> produce the atom coordinates. Then I tried to use the conformation in  
> support directory of charmm(support/membrane/dppc.tar.gz), but the  
> format seemed imcompatible. I also searched the web to find a  
> pre-equilibrated conformation. I found one(dppc_feller_feb99.crd) in
> But there didn't give more information of this conformation(details of  
> the simulation). Anyone could give me some advice?
>
____________________________________________

Simon BERNECHE
B.R. Theoretical Biophysics Laboratory
Weill Medical College of Cornell University

email: [email-masked]
tel:(212)746-4237
fax: (212)746-4843
____________________________________________