[gmx-users] membrane-protein tutorial
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 7 15:39:36 CET 2011
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 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
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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