[gmx-users] amber DNA non-integer charge

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 28 21:06:45 CEST 2011



Kamesh Narasimhan wrote:
> I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are as you mentioned.
> 
> "H1    amber99_17    0.35200    19"
> 
> But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type 
> 
> so what should have been
> 
> amber99_17      1    DG5     H1     19   0.35200    1.008   ; 
> 
> is written by pdb2gmx as
> 
> amber99_25      1    DG5     H1     19     0.4422      1.008   ;
> 
> How can I make amber generate the topology with the right atomtype and charge in this case?. Thanks in advance.
> 

I don't know, but it's not productive to troubleshoot buggy behavior in a 
Gromacs version that is over two years old.  I'd suggest upgrading to the newest 
version (4.5.4, with the appropriate version of the Amber ports) and seeing if 
the behavior persists.  Otherwise, edit the topology manually to correct the error.

-Justin

> my top file:
> 
>  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
>     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
> .....
> .......
> .....
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Monday, August 29, 2011 2:41 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] amber DNA non-integer charge
> 
> 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--
>> gmx-users mailing list    gmx-users at gromacs.org
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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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-- 
========================================

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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