wiki:AddAResidue

Adding a new residue

Here's some conversation excerpts:

Hi Feng,

We will need to model carbohydrates along with the protein. These residues are not currently defined.

Do you have any recommendations on how to proceed?

Thanks, Emre.

Hi Emre,

It is possible to do these calculations. The current approach is to define these molecules in the "newTopParamList".

First, you need to define the mol2 file for the molecule (which can be defined by openbabel) and create the topparm.list. Second, edit the input pdb file so that each of such molecule is seperated by "TER" as seperated chains

I attached some examples.

Best,

Feng

Attached examples: GSH.mol2

File Edit Options Buffers Tools Help
@<TRIPOS>MOLECULE
GSH.pdb
36 35 1 0 0
SMALL
NO_CHARGES


@<TRIPOS>ATOM
      1 CA1        32.9720    3.0670   19.6170 C.3       1 GSH482      0.0000
      2 CA2        30.4640   -1.4490   17.0590 C.3       1 GSH482      0.0000
      3 CA3        30.7120   -3.7330   14.0010 C.3       1 GSH482      0.0000
      4 CB1        32.8030    2.4930   18.1940 C.3       1 GSH482      0.0000
      5 CB2        29.0880   -1.9170   17.5860 C.3       1 GSH482      0.0000
      6 CG1        31.3320    2.0960   17.9930 C.3       1 GSH482      0.0000
      7 SG2        29.1580   -1.8750   19.3850 S.3       1 GSH482      0.0000
      8 CD1        31.1780    0.6020   18.2200 C.2       1 GSH482      0.0000
      9 OE1        31.5550    0.0850   19.2730 O.2       1 GSH482      0.0000
     10 C1         31.8270    4.0430   19.8530 C.2       1 GSH482      0.0000
     11 N1         32.9560    2.0360   20.6580 N.4       1 GSH482      0.0000
     12 C2         30.6490   -1.8830   15.5770 C.2       1 GSH482      0.0000
     13 N2         30.6530   -0.0190   17.1950 N.am      1 GSH482      0.0000
     14 O2         30.7960   -1.0480   14.6410 O.2       1 GSH482      0.0000
     15 C3         32.1060   -4.3120   13.7420 C.2       1 GSH482      0.0000
     16 N3         30.6040   -3.2170   15.3670 N.am      1 GSH482      0.0000
     17 O11        31.0380    3.7730   20.7540 O.co2     1 GSH482      0.0000
     18 O12        31.8130    5.1360   19.0880 O.co2     1 GSH482      0.0000
     19 O31        32.8820   -3.5970   13.0460 O.co2     1 GSH482      0.0000
     20 O32        32.3350   -5.4930   14.1410 O.co2     1 GSH482      0.0000
     21 HA1        33.9161    3.6092   19.6702 H         1 GSH482      0.0000
     22 HB12       33.4389    1.6158   18.0748 H         1 GSH482      0.0000
     23 HB13       33.0813    3.2488   17.4595 H         1 GSH482      0.0000
     24 HG12       31.0242    2.3431   16.9770 H         1 GSH482      0.0000
     25 HG13       30.7085    2.6381   18.7040 H         1 GSH482      0.0000
     26 H2         30.3493    0.5555   16.4218 H         1 GSH482      0.0000
     27 HA2        31.2338   -1.9449   17.6503 H         1 GSH482      0.0000
     28 HB22       28.8840   -2.9319   17.2448 H         1 GSH482      0.0000
     29 HB23       28.3078   -1.2438   17.2307 H         1 GSH482      0.0000
     30 H3         30.4969   -3.8522   16.1449 H         1 GSH482      0.0000
     31 HA32       30.5270   -2.9211   13.2977 H         1 GSH482      0.0000
     32 HA33       29.9659   -4.5136   13.8522 H         1 GSH482      0.0000
     33 H11        32.3704    1.2679   20.3628 H         1 GSH482      0.0000
     34 H12        33.8960    1.7015   20.8147 H         1 GSH482      0.0000
     35 H13        32.5909    2.4278   21.5143 H         1 GSH482      0.0000
     36 HG2        30.3971   -1.5639   19.7759 H         1 GSH482      0.0000
@<TRIPOS>BOND
     1   21    1 1
     2    1    4 1
     3   23    4 1
     4   22    4 1
     5    4    6 1
     6   25    6 1
     7   24    6 1
     8    8    6 1
     9    8    9 2
    10    8   13 am
    11   26   13 1
    12    2   13 1
    13   27    2 1
    14    2    5 1
    15   29    5 1
    16   28    5 1
    17    5    7 1
    18   36    7 1
    19   12    2 1
    20   12   16 am
    21   30   16 1
    22    3   16 1
    23   32    3 1
    24   31    3 1
    25   15    3 1
    26   15   20 2
    27   15   19 2
    28   12   14 2
    29   10    1 1
    30   10   18 2
    31   10   17 2
    32    1   11 1
    33   34   11 1
    34   33   11 1
    35   35   11 1
@<TRIPOS>SUBSTRUCTURE
     1 GSH482     10 RESIDUE           4 A     GSH     0 ROOT

topparam.list

##############################################################
#These are the additional TOPOLOGY files
#For small moleucle, the initial mol2 file much be applied!
#For newly introduced ATOM TYPE, must also SUPPLY
#its NON-BONDED(VDW+SOLV) interactions parameters
##############################################################
MOL     GSH             ./GSH.mol2
Last modified 8 years ago Last modified on Nov 10, 2010 6:44:13 PM