[gmx-users] POPC simulation

[Justin A. Lemkul]

Quoting Moutusi Manna <mou2c_21 at yahoo.co.in>:

>   thanks for reply.I want to perform simulation of popc membrane.
>   Steps which i have done are as follows:
>   1. download popc128a.pdb, popc.it,lipids.itp
>   (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
>   2. download ffgmx_lipids files
>   3.convert POPC of .top & popc.itp into POP as in popc.gro
>   4. #include "ffgmx.itp"
>   #include "lipid.itp"
>   #include "popc.itp"
>   #include "ffgmxnb.itp"
>   #include "ffgmxbon.itp"

These last two lines should already be included in ffgmx.itp, and including them
twice may cause some headaches.

>   ................ in my .top file.
>
>   Now when I perform
>   pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top
>   it shows the error that"Residue 'POP' not found in residue topology
> database".
>   I think that's because of the fact that ffgmx.rtp do not
>   contain "POP" residue ,but it has DPPC residue.
>   Plz suggest how can i solve this problem.
>   thanks.

Use editconf to convert between .pdb and .gro.  You only need pdb2gmx if you
don't have a .top file, but Prof. Tieleman has kindly provided this for you
already, in the form of lipid.itp and popc.itp.

-Justin


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

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