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 <[email protected]
<mailto:[email protected]>> 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
========================================
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