[gmx-users] membrane-protein tutorial

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Dr.Justin
> Yes,I know,it deleted some lipids according to inflateGRO script in the 
> first timethat I used perl command.
> Besides:
> I did iteration 25 times correctly,and no addition or doubling was occured.
> I used the same commands of  25th iteration.of course I changed numberes 
> from 25 to 26 in commands.
> I think it is because I have compacted my lipids more than it is required.
> 

Over-packing your lipids will not cause your coordinate file to magically be 
doubled.

> my commands are as below:
> after doing EM for output of 25th iteration(its output were 
> EM-inflate-26.*) I entered :
> 
> trjconv     -f  EM-inflate-26.trr       -s  EM-inflate-26.tpr      -o   
> EM-inflate-26-trj.gro       -pbc   mol     -ur   compact

Here's the problem.  You're converting a .trr (which presumably has 2 frames) 
and converting it to a multi-frame .gro file.  All you need is to fix the PBC on 
the final frame, i.e. the .gro file that mdrun writes.

-Justin

> perl     inflategro        EM-inflate-26-trj.gro      0.95         
> DPPC      0        system_shrink26.gro      5        area_shrink26.dat
> grompp      -f      minim-strong.mdp       -c        
> system_shrink26.gro        -p    topol.top         -o   EM-inflate-27.tpr
> 
> thanks in advance for your reply
> 
> 
> On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     mohsen ramezanpour wrote:
> 
>         Dear all
> 
>         I am doing Membrane -protein tutorial.
>         Actually I did each step carefully,I could score down my lipids
>         26 times.
>         But there were two problems:
>         1-I get ~77 A for area per lipid in 26th step not 71 as
>         Dr.Justin has said
>         2-I tried to do more iteration to make closer my area per lipid
>         to 71,But I get the following error:
>         Program grompp, VERSION 4.0.7
>         Source code file: ../../../../src/kernel/grompp.c, line: 362
> 
>         Fatal error:
>         number of coordinates in coordinate file (system_shrink26.gro,
>         12876)
>                     does not match topology (topol.top, 6438)
> 
>         I checked and I found program has added some additional DPPC
>         molecules to my system!!
> 
> 
>     InflateGRO does not add lipids, it deletes them.  Whatever you've
>     done has exactly doubled the system.  You've managed to concatenate
>     coordinate files or otherwise manipulate it in some nonsensical way.
>      Without seeing the command you used it's impossible to say.
> 
>     -Justin
> 
> 
>         Besides I get 32 A area per lipid for this step!!!
> 
>         Please let me know what is the reason.
>         Thanks in advance
>         Mohsen
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================