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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