[gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

xi zhao zhaoxiitc2002 at yahoo.com.cn
Mon Apr 12 14:58:17 CEST 2010

my procesure:
1. cat cgprotein cgmembrane>system.gro (using Martini force field)
2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o system_inflatedem.tpr (with strong postion restraint)
4. mdrun
5 in the system_inflatedem.gro , the protein and membrane  separate each other.
please help me !

--- 10年4月12日,周一, Justin A. Lemkul <jalemkul at vt.edu> 写道:

发件人: Justin A. Lemkul <jalemkul at vt.edu>
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
日期: 2010年4月12日,周一,下午8:42

xi zhao wrote:
> Dear Gromacs users:
> I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me!

What does "apart" mean?  If you want free help, you have to make it easy to help you.  That means thorough descriptions of what you're doing, what you're seeing, and if necessary, posting images online (not as attachments!) for us to take a look.  The InflateGRO method should generate a configuration that has molecules separated by a large amount of space, but if there is something else wrong you'll have to provide a better description.


> 4 <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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