Hi Tsjerk,
First of all thanks for your quick and kind reply.
So you say that instead of using:
lipidsx[moltype] = (0, .5, 0, 0, .5, 0, 0, .5, 0,0, .5,
0,0,0, 0,0,0,0, .5, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1)
lipidsy[moltype] = (0, 0, 0, 0, 0, 0, 0, 0, 0,0,0,
0, .5,1, 1,1,1,0,0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0)
lipidsz[moltype] = (6, 7, 7, 8, 9, 9, 10, 11, 11, 12, 13,
13, 10,9, 10,8, 11,5,5, 4, 3, 2, 1, 0, 4, 3,
2, 1, 0)
lipidsa.update({ # 1 2345 6 7 8 91011
121314 1516171819 20 21 22 23 24 25 26
27 28 29
DGDG: (moltype, GB2 GB3 GB1 GA1 GA2 GA3 - - - - - -
- -- - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B
C4B - ),
i should changed it to:
DGDG: (moltype, GA1 GA2 GA3 GB1 GB2 GB3 - - - - - -
- -- - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B
C4B - ),
What about the first three lines? Is it order important?
Also i’m writing an email to your collaborator about how he used insane to
build this mixture membrane (with respect to POPC-MGDG and POPC-SQDG i didn’t
have any kind of problems)
Thanks a lot Tsjerk.
Best,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
On March 25, 2015 at 10:41:48 AM, Tsjerk Wassenaar
(tsje...@gmail.commailto:tsje...@gmail.com) wrote:
Hi Carlos,
Probably it's better to change the order in insane to match up with the
itp. Maybe the definition was based on a different topology than the one in
the martini_v2.0_glycolipids.itp
Alternatively, you can check up with Floris van Eerden, who used insane for
building complex glycolipid membranes (including MGDG and SQDG).
Hope it helps,
Tsjerk
On Wed, Mar 25, 2015 at 10:32 AM, Carlos Navarro Retamal cnava...@utalca.cl
wrote:
Dear gromacs users,
I’m planing to perform several CG simulations of different biological
membranes in the presence of an specific protein.
In order to create the membranes, i’m currently using the insane script to
make different kind of mixture (POPC alone, POPC-MGDG 5:5, POPC-SQDG 5:5,
and POPC-DGDG 5.5) as following:
./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5
-box 10,10,10 -l DGDG:5 -l POPC:5 -sol W -orient
The problem arise when i tried to add ions in order to create a net charge
in the last mixture membrane (POPC-DGDG), using the following command line:
grompp -f ions.mdp -c system.gro -p system.top -o ions.tpr
Getting the following warning message:
Warning: atom name 177 in system.top and system.gro does not match (GA1 -
GB2)
Warning: atom name 178 in system.top and system.gro does not match (GA2 -
GB3)
Warning: atom name 179 in system.top and system.gro does not match (GA3 -
GB1)
Warning: atom name 180 in system.top and system.gro does not match (GB1 -
GA1)
Warning: atom name 181 in system.top and system.gro does not match (GB2 -
GA2)
Warning: atom name 182 in system.top and system.gro does not match (GB3 -
GA3)
(more than 20 non-matching atom names)
Looking into the .itp file (martini_v2.0_glycolipids.itp) i found that the
atoms GA1, GA2, GA3, GB1, GB2 and GB3 are described in a different order
between the *itp file and the *gro file (where first is described the GB2
atom, followed by GB3, GB1, GA1,GA2 and finally GA3) created by insane
script.
My question is, it is ok if i just change the order in the *itp file, to
make it identical as the one found in the *gro file? If not, what should i
do in order to avoid any kind of issue during the simulation?. Thanks in
advance
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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--
Tsjerk A. Wassenaar, Ph.D.
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