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

shivangi nangia shivangi.nangia at gmail.com
Tue May 27 16:36:35 CEST 2014 

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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