[gmx-users] non-matching atom names in CG simulations

Wed Mar 25 10:56:43 CET 2015

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     2    3    4    5   6   7   8   9    10    11    12    13    14   15    16    17    18    19   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.navarro87 at gmail.com or cnavarro at utalca.cl

On March 25, 2015 at 10:41:48 AM, Tsjerk Wassenaar (tsjerkw at gmail.com<mailto:tsjerkw at 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 <cnavarro at 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.navarro87 at gmail.com or cnavarro at utalca.cl
>
> --
> Gromacs Users mailing list
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--
Tsjerk A. Wassenaar, Ph.D.
--
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