[gmx-users] amber DNA non-integer charge

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 28 20:41:30 CEST 2011



Kamesh Narasimhan wrote:
> Hil,
> 
> I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation .  From the webpage of ffamber on NA-simulations, I could see this below instruction
> 
> "However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen".
> 
> I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates. 
> 
> In my top file I can see this residue of the type "amber99_25" . How do I correct for the atom-type and charge in this case ?
> 
> " amber99_25      1    DG5    H5T      2     0.4422      1.008   ; qtot -0.1896"
> 
> 
> My top file section:
> 
>  nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
>      1 amber99_43      1    DG5    O5'      1    -0.6318         16   ; qtot -0.6318
>      2 amber99_25      1    DG5    H5T      2     0.4422      1.008   ; qtot -0.1896
>      3 amber99_11      1    DG5    C5'      3    -0.0069      12.01   ; qtot -0.1965
>      4 amber99_19      1    DG5   H5'1      4     0.0754      1.008   ; qtot -0.1211
>      5 amber99_19      1    DG5   H5'2      5     0.0754      1.008   ; qtot -0.0457
>      6 amber99_11      1    DG5    C4'      6     0.1629      12.01   ; qtot 0.1172
>      7 amber99_19      1    DG5    H4'      7     0.1176      1.008   ; qtot 0.2348
>      8 amber99_44      1    DG5    O4'      8    -0.3691         16   ; qtot -0.1343
>      9 amber99_11      1    DG5    C1'      9     0.0358      12.01   ; qtot -0.0985
>     10 amber99_20      1    DG5    H1'     10     0.1746      1.008   ; qtot 0.0761
>     11 amber99_40      1    DG5     N9     11     0.0577      14.01   ; qtot 0.1338
>     12  amber99_6      1    DG5     C8     12     0.0736      12.01   ; qtot 0.2074
>     13 amber99_24      1    DG5     H8     13     0.1997      1.008   ; qtot 0.4071
>     14 amber99_36      1    DG5     N7     14    -0.5725      14.01   ; qtot -0.1654
>     15  amber99_4      1    DG5     C5     15     0.1991      12.01   ; qtot 0.0337
>     16  amber99_2      1    DG5     C6     16     0.4918      12.01   ; qtot 0.5255
>     17 amber99_41      1    DG5     O6     17    -0.5699         16   ; qtot -0.0444
>     18 amber99_35      1    DG5     N1     18    -0.5053      14.01   ; qtot -0.5497
>     19 amber99_25      1    DG5     H1     19     0.4422      1.008   ; qtot -0.1075

The charge on H1 is wrong.  According to the DG5 .rtp entry (in the version 
4.5.x series), the charge should be 0.352.

-Justin

>     20  amber99_3      1    DG5     C2     20     0.7432      12.01   ; qtot 0.6357
>     21 amber99_38      1    DG5     N2     21     -0.923      14.01   ; qtot -0.2873
>     22 amber99_17      1    DG5    H21     22     0.4235      1.008   ; qtot 0.1362
>     23 amber99_17      1    DG5    H22     23     0.4235      1.008   ; qtot 0.5597
>     24 amber99_37      1    DG5     N3     24    -0.6636      14.01   ; qtot -0.1039
>     25  amber99_4      1    DG5     C4     25     0.1814      12.01   ; qtot 0.0775
>     26 amber99_11      1    DG5    C3'     26     0.0713      12.01   ; qtot 0.1488
>     27 amber99_19      1    DG5    H3'     27     0.0985      1.008   ; qtot 0.2473
>     28 amber99_11      1    DG5    C2'     28    -0.0854      12.01   ; qtot 0.1619
>     29 amber99_18      1    DG5   H2'1     29     0.0718      1.008   ; qtot 0.2337
>     30 amber99_18      1    DG5   H2'2     30     0.0718      1.008   ; qtot 0.3055
>     31 amber99_44      1    DG5    O3'     31    -0.5232         16   ; qtot -0.2177
>     ....
>     ..... 
> 
> My pdb file section:
> ATOM      1  C5' DG5 A   1      28.937 -10.596 -28.986  1.00 95.46           C
> ATOM      2  O5' DG5 A   1      30.060 -10.216 -29.774  1.00 95.82           O
> ATOM      3  C4' DG5 A   1      29.239 -11.863 -28.212  1.00101.28           C
> ATOM      4  O4' DG5 A   1      30.545 -11.736 -27.597  1.00102.88           O
> ATOM      5  C3' DG5 A   1      28.300 -12.150 -27.052  1.00100.37           C
> ATOM      6  O3' DG5 A   1      28.363 -13.527 -26.704  1.00104.13           O
> ATOM      7  C2' DG5 A   1      28.913 -11.282 -25.960  1.00 95.28           C
> ATOM      8  C1' DG5 A   1      30.395 -11.553 -26.200  1.00100.67           C
> ATOM      9  N1  DG5 A   1      34.400 -10.292 -23.339  1.00 88.74           N
> ATOM     10  C2  DG5 A   1      33.795 -11.515 -23.502  1.00 92.09           C
> ATOM     11  N2  DG5 A   1      34.320 -12.542 -22.818  1.00 92.20           N
> ATOM     12  N3  DG5 A   1      32.745 -11.722 -24.284  1.00100.66           N
> ATOM     13  C4  DG5 A   1      32.342 -10.585 -24.901  1.00101.19           C
> ATOM     14  C5  DG5 A   1      32.877  -9.321 -24.804  1.00 97.04           C
> ATOM     15  C6  DG5 A   1      33.999  -9.114 -23.965  1.00 93.19           C
> ATOM     16  O6  DG5 A   1      34.613  -8.059 -23.751  1.00 94.32           O
> ATOM     17  N7  DG5 A   1      32.171  -8.426 -25.598  1.00 94.27           N
> ATOM     18  C8  DG5 A   1      31.241  -9.155 -26.150  1.00 97.12           C
> ATOM     19  N9  DG5 A   1      31.282 -10.474 -25.771  1.00100.33           N
> 
>   ....
>    ..... 
> 
> 
> thanks
> kamesh-- 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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