[gmx-users] Backward (CG to atomistic), no charmm27

[shivangi nangia]

Hello,

Thanks for the replies.

I created an atomistic .top file for my system (POPC and protein)
successfully using charmm36 with initram.sh.

Now I tried to change charmm36 to charmm27 in the topology file.

i.e. # include "charmm27/forcefield.itp" *instead of * #include
"ffcharmm36.itp"

I tried to run this using grompp:

grompp_mpi -f minim.mdp -c system_aa.gro -p prot_popc_bkmapped.top -o em.tpr


*I get the error:*


*Program grompp_mpi, VERSION 4.6.1*

*Source code file:
/admin/sw-src/Gromacs/gromacs-4.6.1/src/kernel/toppush.c, line: 1336*


*Fatal error:*

*Atomtype OSLP not found*

*For more information and tips for troubleshooting, please check the
GROMACS*

*website at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>*


So, on trying to find atom type "OSLP" I found it in ffbonded.itp and
ffnonbonded.itp.

OSLP is part of POPC.

Also, both these .itp files mention that these are new parameters/atom
types are in charmm36 which is not found in charmm27.


Thanks in advance for the help.



Just as an example:

fbonded.itp:OSLP CTL2 CTL1 OSL 9 180.00 2.539688 3 ; New

ffbonded.itp:OSLP CTL2 CTL1 OSL 9 60.00 1.062736 2 ; New

ffbonded.itp:OSLP CTL2 CTL1 OSL 9 180.00 8.434944 1 ; New

ffbonded.itp:OSLP CTL2 CTL2 OSL 9 0.00 0.0 4 ; New

ffbonded.itp:OSLP CTL2 CTL2 OSL 9 180.00 2.539688 3 ; New

ffbonded.itp:OSLP CTL2 CTL2 OSL 9 60.00 1.062736 2 ; New

ffbonded.itp:OSLP CTL2 CTL2 OSL 9 180.00 8.434944 1 ; New

ffbonded.itp:NH3L CTL2 CTL2 OSLP 9 180.00 2.9288 1 ; New

ffbonded.itp:NTL CTL2 CTL2 OSLP 9 180.00 13.8072 1 ; New

ffbonded.itp:NTL CTL2 CTL2 OSLP 9 180.00 -1.6736 3 ; New

ffbonded.itp:X CTL1 OSLP X 9 0.00 0.0 3 ; New

ffbonded.itp:X CTL2 OSLP X 9 0.00 0.0 3 ; New

ffbonded.itp:X CTL3 OSLP X 9 0.00 0.0 3 ; New

ffnonbonded.itp:; Added new and changed old atomtypes and pairtypes (OSL,
OSLP, HBL and CCL) - Thomas Pigot July 2010

ffnonbonded.itp:OSLP 8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27

ffnonbonded.itp:CP1 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CP2 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CP3 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CPT OSLP 1 0.316269044940 0.396929091904 ; Not in C27

ffnonbonded.itp:CT1 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT2 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT3 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT1x OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT2x OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CT3x OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:HP OSLP 1 0.268000152391 0.22916711806 ; Not in C27

ffnonbonded.itp:N OSLP 1 0.311814551349 0.0132309697301 ; Not in C27

ffnonbonded.itp:NH1 OSLP 1 0.285087589805 0.591706954497 ; Not in C27

ffnonbonded.itp:O OSLP 1 0.271724109033 0.45833423612 ; Not in C27

ffnonbonded.itp:OB OSLP 1 0.271724109033 0.45833423612 ; Not in C27

ffnonbonded.itp:OCA OSLP 1 0.271724109033 0.45833423612 ; Not in C27

ffnonbonded.itp:CTL1 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CTL2 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CTL3 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:CTL5 OSLP 1 0.316269044940 0.132309697301 ; Not in C27

ffnonbonded.itp:OBL OSLP 1 0.271724109033 0.45833423612 ; Not in C27



Thanks,
sxn


On Mon, May 26, 2014 at 2:48 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi sxn,
>
> That's a bit odd. Possibly the version of the CHARMM POPC mapping on
> cgmartini.nl does not have charmm27 under the [ mapping ], but it should
> be
> added then. There is no difference in terms of backmapping. Anyway, you can
> use the charmm36 like you did. It will use your force field settings as
> dictated by the atomistic topology. There is nothing specific for charmm36
> versus charmm27 in backward or initram.
>
> Cheers,
>
> Tsjerk
>
>
>
>
> On Mon, May 26, 2014 at 8:20 PM, shivangi nangia
> <shivangi.nangia at gmail.com>wrote:
>
> > Hello,
> >
> > I was able to convert my coarse grained system to all-atom using the
> > backward script.
> > However, it (Mapping folder) only had option for charmm36.
> >
> > I have an all-atom .gro file and .top file for charmm36 but I need t run
> my
> > simulations with charmm27.
> >
> > Doing pdb2gmx with all-tom .gro file runs into error which I believe is
> for
> > mismatch in atom types between charmm36 and 27.
> >
> > Also,on using the command (./initram.sh -f system.gro -f system_aa.top
> -po
> > backmapped.top -from martini -to charmm27)  handled the protein part of
> the
> > system but ran into error for POPC, but changing -from martini -to
> charmm36
> >  successfully converted to all atom.
> >
> > Please suggest.
> >
> > Thanks,
> > sxn
> > --
> > Gromacs Users mailing list
> >
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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