[gmx-users] Azurin protein attached to metal atom of Cu.

[Justin Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 4/30/14, 6:37 AM, Alessia Giuliani wrote:
>
> hello,
> first of all thanks for reply.
> I send to you the specialbond.dat :
>
>
> 11
> CYS    SG    1     CYS      SG    1      0.2    CYS2    CYS2
> CYS    SG    1    HEM       FE    2      0.25    CYS2    HEME
> CYS    SG    1     HEM     CAB   1    0.18    CYS2    HEME
> CYS    SG    1     HEM     CAC   1    0.18    CYS2    HEME
> HIS     NE2    1    HEM     FE  1       0.2    HIS1    HEME
> MET    SD    1     HEM      FE    1      0.24    MET    HEME
> CO      C       1     HEME    FE   1    0.19    CO      HEME
> CYM   SG      1     CYM     SG    1    0.2     CYS2    CYS2
> CCC   SG    1      CU       CU    1      0.21  CCC       CU
> HHH   ND1    1    CU       CU    1      0.19    HHH       CU
> HHM   ND1    1    CU       CU    1      0.21    HHM       CU
>
>
> I added the last three rows for the cu ties with its ligands.
> In the final section of the ffbonded.it I called covalent bonds :
>
> ; bond-, angle- and dihedraltypes for specbonds:
> [ bondtypes ]
> S     S      2    gb_33
> NR     FE     2    gb_32
> ; cystine - heme link (is CR1-S, use CH2-S):
> S     CR1     2    gb_30
> ; his - cu link
> NR         CU     2    gb_48
> NR      CU     2    gb_49
> ; cystine - cu link
> S CU     2    gb_50
> ;
> ; CYSTEINE - ZN LINK
> S     ZN     2    gb_52
> S     ZN     2    gb_54
> S     ZN     2    gb_55
> ; HIS - ZN LINK
> NR         ZN     2    gb_53
> [ angletypes ]
> CH1    CH2    S     2   ga_15
> CH2    S      S     2   ga_5
> CR1    NR    FE     2    ga_33
> NR     FE    NR     2   ga_16
> ; cystine - heme link (is CH2-S-CR1, use CH2-S-CH2):
> CH2    S     CR1    2   ga_3
> ; cystine - heme link (is S-CR1-C/CH2, use CHn-CH2-S):
> S      CR1   C      2   ga_15
> S      CR1   CH2    2   ga_15
> ; for hisb, his2 and CYS2 of azurin :
> NR        CU    NR          2   ga_47
> S         CU    NR 2   ga_48
> S         CU    NR          2   ga_49
> CR1       NR    CU          2   ga_50
> C         NR    CU          2   ga_51
> CR1       NR    CU          2   ga_52
> C         NR    CU          2   ga_53
> CH2       S CU          2   ga_54
> ;
> ; ZINC FINGER
> S         ZN    NR          2   ga_56
> S         ZN    S           2   ga_57
> S         ZN    S           2   ga_58
> S         ZN    NR          2   ga_59
> CR1       NR    ZN 2   ga_60
> C         NR    ZN          2   ga_61
> CH2       S     ZN          2   ga_62
> CH2       S     ZN          2   ga_63
> CH2       S     ZN          2   ga_64
> ;
> [ dihedraltypes ]
> S      S      1   gd_10
> NR     FE     1   gd_18
> CH2    S      1   gd_13
> ; cystine - heme link (is CH2-S-CR1-C, use -CH2-S-):
> CR1    S      1   gd_13
> ; for hisb, his2 and CYS2 of azurin :
> NR     C          1   gd_22
> NR     CR1        1   gd_23
> NR    C          1   gd_24
> NR    CR1        1   gd_25
> S       CH2        1   gd_13
>
>
> grompp in theory should read Special bond from  file .dat and then assign the
> covalent bonds that reads in the ffbonded.itp file , but it does not. When I do

So are you saying that there is no entry in [bonds] for these interactions?  If 
that's the case, then the reference distance in specbond.dat is not suitable and 
the bonds aren't being written.  However, the assertion that bond is not written 
is in contrast to this observation:

> an analysis of distances, these remain fixed , the atoms do not vibrate .
> This also happens to the bridge sulfide which is enabled by default in the file
> specailbond.dat when you download the program .
>

How are you treating the bonds during the simulation?  If you're using 
"constraints = all-bonds," then this is precisely the outcome you should expect; 
all the requested bonds are indeed present and are being kept fully rigid by the 
constraint algorithm.  If there were no bond(s) produced by specbond.dat, then 
these distances would not be constant.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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