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

Wed May 28 18:57:33 CEST 2014

Hi sxn,

As I said, there is nothing specific in backward/initram with respect to
charmm27 versus charmm36. You can use -to charmm36 to backmap against your
charmm27 topology andget a charmm27 system. We may have missed adding
charmm27 as tag in one of the mappings, and we haven't checked backmapping
to charmm27, as we regard it superseded by charmm36.

Cheers,

Tsjerk
On May 28, 2014 6:28 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
wrote:

> Dear Justin and Tsjerk,
>
> Just as a gentle reminder, could you please answer my query.
>
> Thanks for your time.
>
> -sxn
>
>
>
> On Tue, May 27, 2014 at 10:34 AM, shivangi nangia <
> shivangi.nangia at gmail.com
> > wrote:
>
> > Hello,
> >
> > Sorry for multiple e-mails.
> >
> > Also, on trying to use initram.sh as:
> >
> > ./my_intiram.sh -f prot_popc_cg.gro -p prot_popc_aa.top -po
> > prot_popc_bkmapped.top -from martini -to charmm27
> >
> >
> > where the prot_popc_aa.top file contains commands to include charmm27.ff
> > parameters,
> >
> > ./my_intiram.sh -f prot_popc_cg.gro -p prot_popc_aa.top -po
> > prot_popc_bkmapped.top -from martini -to charmm27
> >
> >
> > I get the error:
> >
> > R*esidues defined for transformation from martini to charmm27:*
> >
> > *Traceback (most recent call last):*
> >
> > *  File "/inverse_cg/try2/backward.py", line 821, in <module>*
> >
> > *    raise ValueError, "Unknown residue: %s\n"%resn*
> >
> > *ValueError: Unknown residue: ALA*
> >
> >
> >  ALA is the first amino acid of my protein, I m guessing it will be
> > unable to trace other residues too.
> >
> > Kindly suggest.
> >
> > Thanks,
> > sxn
> >
> > On Tue, May 27, 2014 at 10:14 AM, shivangi nangia <
> > shivangi.nangia at gmail.com> wrote:
> >
> >> 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.
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>
> >>
> >
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