[gmx-users] membrane-protein tutorial

[mohsen ramezanpour]

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.

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
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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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