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

Wed May 28 18:25:07 CEST 2014

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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>>
>>
>