terminal phosphate group in RNA from David A. Case on 2003-01-24 (Amber Archive Jan 2003)

From: David A. Case <case_at_scripps.edu>
Date: Fri 24 Jan 2003 16:03:06 -0800

On Thu, Jan 16, 2003, Mahadevan Seetharaman wrote:
>
> Can someone give me suggestions for treating a terminal phosphate group in
> a RNA molecule.
>
> I want a net charge of -1 and I am not sure about the individual charges
> and atom types on the phosphorous and the oxygen atoms... any reference
> on this issue would also be greatly appreciated.
>

This is not as easy as it should be. You basically have to create a terminal
phosphate-capped nucleotide, and link it in.

I'v attached some files we have used for a 5' guanine with an terminal
phosphate, for RNA simulations. The appropriate commands in leap would be:

loadAmberPrep 5gp.prepi
source leaprc.rna.ff99
loadAmberParams frcmod.5gp
x = loadpdb 5gp_test.pdb
saveAmberParm x prmtop prmcrd

Notes:

With just an obvious phosphate force field, bad things can happen with the
terminal H atom. We "cheated" by adding an artificial P--H bond to keep the
geometry of the terminal P-O-H group fixed (as in TIP3P water, for example).

Because of the above, you have to load this prep file *before* loading the
leaprc file. This is a bug in leap, which will get fixed, but for now, this
workaround should do. (Try the other order to see the problem.)

Charges above are RESP for this nucleotide; you would need to do something
similar for the A,C,U if you needed those...

.hope this helps...good luck...dac

[Note: I forgot that the reflector won't take attachments....files are
added below as text instead....]

-- 
==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
====================== 5gp.prepi==========================================
 0 0 0
 5' guanine with capped phosphate
5GP.res
5GP  INT     0
CHANGE   NOMIT DU   BEG 
   0.00000
   1   DUMM  DU    M      0.000000  0.000000  0.000000  0.0
   2   DUMM  DU    M      1.000000  0.000000  0.000000  0.0
   3   DUMM  DU    M      1.000000  1.000000  0.000000  0.0
   4   H5T   HO    M      1.404339  0.042249  0.165634    0.396800
   5   O3P   OH    E      1.114476  0.908491  -0.241311    -0.721900
   6   P     P     M      2.314489  1.776673  -0.478436    1.320100
   7   O1P   O2    E      1.933410  3.073374  -1.081549    -0.816600
   8   O2P   O2    E      3.156547  0.871841  -1.292450    -0.816600
   9   O5'   OS    M      2.994369  2.142475  0.922974    -0.558300
   10  C5'   CT    M      2.156035  2.551837  2.019887    0.055800
   11  H5'1  H1    E      1.452687  1.753841  2.257803    0.067900
   12  H5'2  H1    E      1.604968  3.450028  1.741178    0.067900
   13  C4'   CT    M      3.008252  2.847921  3.243186    0.106500
   14  H4'   H1    E      2.447118  3.477373  3.933851    0.117400
   15  O4'   OS    S      3.228121  1.605168  3.977231    -0.354800
   16  C1'   CT    3      4.558614  1.150950  3.777548    0.019100
   17  H1'   H2    E      5.072002  1.095281  4.737461    0.200600
   18  C2'   CT    B      5.230443  2.095696  2.779425    0.067000
   19  H2'1  H1    E      5.668211  2.081313  1.781301    0.097200
   20  O2'   OH    S      6.272982  2.049941  3.757136    -0.613900
   21  HO'2  HO    E      6.759278  1.235228  3.610987    0.418600
   22  N9    N*    B      4.499533  -0.267934  3.326576    0.049200
   23  C4    CB    B      4.673998  -1.376548  4.117501    0.122200
   24  C5    CB    B      4.535095  -2.474583  3.310330    0.174400
   25  C6    C     B      4.665031  -3.772051  3.872552    0.477000
   26  O6    O     E      4.578059  -4.865457  3.315956    -0.559700
   27  N1    NA    B      4.925924  -3.709096  5.246587    -0.478700
   28  H1    H     E      5.032526  -4.575560  5.734311    0.342400
   29  C2    CA    S      5.047712  -2.547461  5.981551    0.765700
   30  N2    N2    B      5.299265  -2.702442  7.288571    -0.967200
   31  H21   H     E      5.396738  -3.573950  7.789643    0.436400
   32  H22   H     E      5.381214  -1.857324  7.835527    0.436400
   33  N7    NB    E      4.278741  -2.081203  2.002035    -0.570900
   34  N3    NC    E      4.927829  -1.332945  5.452892    -0.632300
   35  C8    CK    S      4.267504  -0.772686  2.063331    0.137400
   36  H8    H5    E      4.096308  -0.099877  1.236033    0.164000
   37  C3'   CT    M      4.415606  3.377827  2.961306    0.202200
   38  H3'   H1    E      4.412072  3.941489  2.028369    0.061500
   39  O3'   OS    M      5.029898  4.128649  3.998279    -0.524600
LOOP
 O3P  P   
 C2'  C3' 
 C2   N3  
 C8   N7  
IMPROPER
 C4   C8   N9   C1' 
 H8   N9   C8   N7  
 C6   C4   C5   N7  
 C5   N1   C6   O6  
 C6   C2   N1   H1  
 N2   N1   C2   N3  
 C2   H21  N2   H22 
 C5   N9   C4   N3  
 -M   O3P  H5T  P   
DONE
STOP
================== frcmod.5gp ============================================
#   parameters for 5' guanine with phospphate group
BOND
P - HO    300.0   2.1200
ANGLE
P - HO - OH   0.0      0.00
O2 - P - HO   0.0      0.00
OS - P - HO   0.0      0.00
OH - P - HO   0.0      0.00
 
DIHE
OS-P-HO-OH    2    0.00             0        2.0
O2-P-HO-OH    2    0.00             0        2.0 
====================  5gp_test.pdb===========================================
ATOM      1  P   5GP A   1     -11.508 -25.691  -0.634  1.00  0.00           P  
ATOM      2  O1P 5GP A   1     -10.812 -25.657  -1.940  1.00  0.00           O  
ATOM      3  O2P 5GP A   1     -12.742 -24.897  -0.437  1.00  0.00           O  
ATOM      4  O5* 5GP A   1     -10.453 -25.271   0.508  1.00  0.00           O  
ATOM      5  C5* 5GP A   1      -9.926 -23.963   0.550  1.00  0.00           C  
ATOM      6  C4* 5GP A   1      -8.954 -23.845   1.721  1.00  0.00           C  
ATOM      7  O4* 5GP A   1      -7.803 -24.643   1.522  1.00  0.00           O  
ATOM      8  C3* 5GP A   1      -8.414 -22.431   1.869  1.00  0.00           C  
ATOM      9  O3* 5GP A   1      -9.347 -21.558   2.467  1.00  0.00           O  
ATOM     10  C2* 5GP A   1      -7.199 -22.695   2.739  1.00  0.00           C  
ATOM     11  O2* 5GP A   1      -7.527 -22.689   4.110  1.00  0.00           O  
ATOM     12  C1* 5GP A   1      -6.755 -24.092   2.307  1.00  0.00           C  
ATOM     13  N9  5GP A   1      -5.506 -24.023   1.526  1.00  0.00           N  
ATOM     14  C8  5GP A   1      -5.344 -23.903   0.170  1.00  0.00           C  
ATOM     15  N7  5GP A   1      -4.097 -23.877  -0.212  1.00  0.00           N  
ATOM     16  C5  5GP A   1      -3.380 -23.986   0.976  1.00  0.00           C  
ATOM     17  C6  5GP A   1      -1.977 -24.014   1.190  1.00  0.00           C  
ATOM     18  O6  5GP A   1      -1.075 -23.949   0.356  1.00  0.00           O  
ATOM     19  N1  5GP A   1      -1.671 -24.132   2.538  1.00  0.00           N  
ATOM     20  C2  5GP A   1      -2.598 -24.216   3.557  1.00  0.00           C  
ATOM     21  N2  5GP A   1      -2.114 -24.323   4.802  1.00  0.00           N  
ATOM     22  N3  5GP A   1      -3.919 -24.192   3.356  1.00  0.00           N  
ATOM     23  C4  5GP A   1      -4.235 -24.075   2.045  1.00  0.00           C  
ATOM     35  P    RG A   2      -9.009 -19.995   2.665  1.00  0.00           P  
ATOM     36  O1P  RG A   2     -10.162 -19.355   3.337  1.00  0.00           O  
ATOM     37  O2P  RG A   2      -8.523 -19.464   1.373  1.00  0.00           O  
ATOM     38  O5*  RG A   2      -7.773 -20.012   3.697  1.00  0.00           O  
ATOM     39  C5*  RG A   2      -7.955 -20.395   5.043  1.00  0.00           C  
ATOM     40  C4*  RG A   2      -6.619 -20.349   5.783  1.00  0.00           C  
ATOM     41  O4*  RG A   2      -5.656 -21.151   5.126  1.00  0.00           O  
ATOM     42  C3*  RG A   2      -6.019 -18.949   5.825  1.00  0.00           C  
ATOM     43  O3*  RG A   2      -6.615 -18.142   6.818  1.00  0.00           O  
ATOM     44  C2*  RG A   2      -4.568 -19.283   6.118  1.00  0.00           C  
ATOM     45  O2*  RG A   2      -4.334 -19.420   7.501  1.00  0.00           O  
ATOM     46  C1*  RG A   2      -4.369 -20.620   5.410  1.00  0.00           C  
ATOM     47  N9   RG A   2      -3.612 -20.434   4.158  1.00  0.00           N  
ATOM     48  C8   RG A   2      -4.086 -20.202   2.893  1.00  0.00           C  
ATOM     49  N7   RG A   2      -3.152 -20.087   1.992  1.00  0.00           N  
ATOM     50  C5   RG A   2      -1.972 -20.255   2.710  1.00  0.00           C  
ATOM     51  C6   RG A   2      -0.625 -20.235   2.259  1.00  0.00           C  
ATOM     52  O6   RG A   2      -0.205 -20.062   1.116  1.00  0.00           O  
ATOM     53  N1   RG A   2       0.263 -20.444   3.304  1.00  0.00           N  
ATOM     54  C2   RG A   2      -0.095 -20.650   4.621  1.00  0.00           C  
ATOM     55  N2   RG A   2       0.905 -20.836   5.493  1.00  0.00           N  
ATOM     56  N3   RG A   2      -1.364 -20.671   5.045  1.00  0.00           N  
ATOM     57  C4   RG A   2      -2.243 -20.467   4.037  1.00  0.00           C

Received on Fri Jan 24 2003 - 16:03:06 PST