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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@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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--
========================================
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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