[gmx-users] membrane-protein tutorial
ramezanpour.mohsen at gmail.com
Mon Mar 7 15:58:04 CET 2011
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!!
What do you think?
Thanks in advance
On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul <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.
>> I did iteration 25 times correctly,and no addition or doubling was
>> 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.
> 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,
>> 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.
>> Besides I get 32 A area per lipid for this step!!!
>> Please let me know what is the reason.
>> Thanks in advance
>> -- ========================================
>> 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
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users