[gmx-users] membrane-protein tutorial
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Mon Mar 7 16:02:56 CET 2011
Ok.Thank you very much
On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.justin
>> Thank you.You are right.
>> I did what you said.
>>
>> please let me know the answer of my other question in first email:
>> I am doing iteration more than 26 times that you said in your tutorial.
>> I am in 28th step now and my area per lipid is 63 and I think it is
>> lowering everytimes I do iteration.
>> In the other words it seems it dosen't converge!!
>>
>
> It won't. InflateGRO does what you tell it. If you keep squishing the
> lipids, it will happily create an unstable system. You have to know when to
> stop.
>
> -Justin
>
> What do you think?
>> Thanks in advance
>>
>> On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> 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>
>> <mailto: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> <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 <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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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