Re: Farnesylated Cysteine

From: Xu, Shenyuan (xus2_at_miamioh.edu)
Date: Wed Sep 23 2020 - 20:39:05 CDT

Dear Josh,

I fixed it based on your suggestions. Alternatively, I just appended all
the stream files from CGenFF and it also worked. Maybe the angle parameters
are in one of the stream files.

Thanks!

Shen

On Mon, Sep 21, 2020 at 12:23 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Hi Shen,
>
> What atoms do these indices represent? I think I see this combination for
> atoms C14, C13 and C15 at the end of the tail, which would indeed have this
> angle present. The angles and dihedrals should be similar to what you'd see
> for the other isoprene units, where the atomtypes are slightly different:
> CG321, CG2D1, and CG331. If it were me, I'd use this analogy argument to
> duplicate the needed parameters, and would feel confident doing so because
> of the planar topology around CG2D1 atoms. To be honest though, I'm a bit
> surprised that CGenFF atomtypes are being used for something that is
> obviously lipid-like. The last time I looked at isoprenes, I used CEL1
> instead of CG2D1, and built up parameters by analogy.
>
> -Josh
>
> -Josh
>
> -Josh
>
> On Sun, Sep 20, 2020 at 9:58 AM Xu, Shenyuan <xus2_at_miamioh.edu> wrote:
>
>> Hello everyone,
>> I tried to mutate cysteine to farnesylated cysteine, and successfully
>> generated the mutation by psfgen. After I combine the protein, mg, water,
>> gdp using psfgen, then minimize it in namd, it showed the error "unable to
>> find the angle parameter". The toppar used for the farnesylated cysteine is
>> from "toppar_all36_lipid_prot.str".
>>
>> Here is the mutation part for psfgen:
>> #load the topology files#
>> topology top_all36_prot.rtf
>> topology top_all36_na.rtf
>> topology top_all36_carb.rtf
>> topology top_all36_cgenff.rtf
>> topology toppar_water_ions.str
>> topology toppar_all36_lipid_prot.str
>> topology toppar_all36_na_nad_ppi.str
>>
>> segment PRO {
>> first NTER
>> last CTER
>> pdb $pdbname
>> mutate [string trimleft $mutpos 0] CYSF
>> }
>> coordpdb $pdbname PRO
>> guesscoord
>>
>> Here is the remarks from the psf file:
>> REMARKS original generated structure x-plor psf file
>> REMARKS 2 patches were applied to the molecule.
>> REMARKS topology ../top_all36_prot.rtf
>> REMARKS topology ../top_all36_na.rtf
>> REMARKS topology ../top_all36_carb.rtf
>> REMARKS topology ../top_all36_cgenff.rtf
>> REMARKS topology ../toppar_all36_lipid_prot.str
>> REMARKS topology ../toppar_all36_na_nad_ppi.str
>> REMARKS topology ../toppar_water_ions.str
>> REMARKS segment PRO { first NTER; last CTER; auto angles dihedrals }
>> REMARKS segment GDP { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment MG { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment SOLV { first NONE; last NONE; auto none }
>> REMARKS defaultpatch NTER PRO:1
>> REMARKS defaultpatch CTER PRO:188
>>
>> Here is the log file from the energy minimization that contains the
>> error:
>> Info: PARAMETER file: CHARMM format!
>> Info: PARAMETERS ../par_all36_prot.prm
>> Info: PARAMETERS ../par_all36_na.prm
>> Info: PARAMETERS ../par_all36_lipid.prm
>> Info: PARAMETERS ../par_all36_carb.prm
>> Info: PARAMETERS ../par_all36_cgenff.prm
>> Info: PARAMETERS ../par_water_ions.prm
>> Info: PARAMETERS ../toppar_all36_lipid_prot.str
>> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
>>
>> Warning: DUPLICATE ANGLE ENTRY FOR CD-CT2-NH2
>> PREVIOUS VALUES k=50 theta0=107 k_ub=0 r_ub=0
>> USING VALUES k=52 theta0=108 k_ub=0 r_ub=0
>> Info: SUMMARY OF PARAMETERS:
>> Info: 970 BONDS
>> Info: 2865 ANGLES
>> Info: 7022 DIHEDRAL
>> Info: 200 IMPROPER
>> Info: 6 CROSSTERM
>> Info: 359 VDW
>> Info: 77 VDW_PAIRS
>> Info: 0 NBTHOLE_PAIRS
>> Warning: Ignored 95 bonds with zero force constants.
>> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG331 CG2D1 CG331 (ATOMS
>> 3000 2999 3004).
>>
>> And I think the angle parameter is missing in
>> the toppar_all36_lipid_prot.str.
>>
>> Thanks for any suggestions and comments.
>>
>> Shen
>>
>

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