[gmx-users] amber DNA non-integer charge
Kamesh Narasimhan
g0701207 at nus.edu.sg
Sun Aug 28 21:01:38 CEST 2011
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.
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--
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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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