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.
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 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]> 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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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