subject:"RE\: \[gmx\-users\] amber DNA non\-integer charge"

RE: [gmx-users] amber DNA non-integer charge

2011-08-29 Thread Kamesh Narasimhan

Yes, you were right, upgrading it to 4.5.4 made sure the atom types/charges in 
the DNA termini were recognized correctly. This time the topology got generated 
with integer charges.

thanks


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 3:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] amber DNA non-integer charge

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.

 H1amber99_170.3520019

 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  1DG5 H1 19   0.352001.008   ;

 is written by pdb2gmx as

 amber99_25  1DG5 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  1DG5O5'  1-0.6318 16   ; qtot 
 -0.6318
  2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
 -0.1896
  3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
 -0.1965
  4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
 -0.1211
  5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
 -0.0457
  6 amber99_11  1DG5C4'  6 0.1629  12.01   ; qtot 
 0.1172
  7 amber99_19  1DG5H4'  7 0.1176  1.008   ; qtot 
 0.2348
  8 amber99_44  1DG5O4'  8-0.3691 16   ; qtot 
 -0.1343
  9 amber99_11  1DG5C1'  9 0.0358  12.01   ; qtot 
 -0.0985
 10 amber99_20  1DG5H1' 10 0.1746  1.008   ; qtot 
 0.0761
 11 amber99_40  1DG5 N9 11 0.0577  14.01   ; qtot 
 0.1338
 12  amber99_6  1DG5 C8 12 0.0736  12.01   ; qtot 
 0.2074
 13 amber99_24  1DG5 H8 13 0.1997  1.008   ; qtot 
 0.4071
 14 amber99_36  1DG5 N7 14-0.5725  14.01   ; qtot 
 -0.1654
 15  amber99_4  1DG5 C5 15 0.1991  12.01   ; qtot 
 0.0337
 16  amber99_2  1DG5 C6 16 0.4918  12.01   ; qtot 
 0.5255
 17 amber99_41  1DG5 O6 17-0.5699 16   ; qtot 
 -0.0444
 18 amber99_35  1DG5 N1 18-0.5053  14.01   ; qtot 
 -0.5497
 19 amber99_25  1DG5 H1 19 0.4422  1.008   ; qtot 
 -0.1075
 20  amber99_3  1DG5 C2 20 0.7432  12.01   ; qtot 
 0.6357
 21 amber99_38  1DG5 N2 21 -0.923  14.01   ; qtot 
 -0.2873
 22 amber99_17  1DG5H21 22 0.4235  1.008   ; qtot 
 0.1362
 23 amber99_17  1DG5H22 23 0.4235  1.008   ; qtot 
 0.5597
 24 amber99_37  1DG5 N3 24-0.6636  14.01   ; qtot 
 -0.1039
 25  amber99_4  1DG5 C4 25 0.1814  12.01   ; qtot 
 0.0775
 26 amber99_11  1DG5C3' 26 0.0713  12.01   ; qtot 
 0.1488
 27 amber99_19  1DG5H3' 27 0.0985  1.008   ; qtot 
 0.2473
 28 amber99_11  1DG5C2' 28-0.0854  12.01   ; qtot 
 0.1619
 29 amber99_18  1DG5   H2'1 29 0.0718  1.008   ; qtot 
 0.2337
 30 amber99_18  1DG5   H2'2 30 0.0718  1.008   ; qtot 
 0.3055
 31 amber99_44  1DG5O3' 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

RE: [gmx-users] amber DNA non-integer charge

2011-08-28 Thread Kamesh Narasimhan

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  1DG5H5T  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  1DG5O5'  1-0.6318 16   ; qtot 
-0.6318
 2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
-0.1896
 3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
-0.1965
 4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
-0.1211
 5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
-0.0457
 6 amber99_11  1DG5C4'  6 0.1629  12.01   ; qtot 
0.1172
 7 amber99_19  1DG5H4'  7 0.1176  1.008   ; qtot 
0.2348
 8 amber99_44  1DG5O4'  8-0.3691 16   ; qtot 
-0.1343
 9 amber99_11  1DG5C1'  9 0.0358  12.01   ; qtot 
-0.0985
10 amber99_20  1DG5H1' 10 0.1746  1.008   ; qtot 
0.0761
11 amber99_40  1DG5 N9 11 0.0577  14.01   ; qtot 
0.1338
12  amber99_6  1DG5 C8 12 0.0736  12.01   ; qtot 
0.2074
13 amber99_24  1DG5 H8 13 0.1997  1.008   ; qtot 
0.4071
14 amber99_36  1DG5 N7 14-0.5725  14.01   ; qtot 
-0.1654
15  amber99_4  1DG5 C5 15 0.1991  12.01   ; qtot 
0.0337
16  amber99_2  1DG5 C6 16 0.4918  12.01   ; qtot 
0.5255
17 amber99_41  1DG5 O6 17-0.5699 16   ; qtot 
-0.0444
18 amber99_35  1DG5 N1 18-0.5053  14.01   ; qtot 
-0.5497
19 amber99_25  1DG5 H1 19 0.4422  1.008   ; qtot 
-0.1075
20  amber99_3  1DG5 C2 20 0.7432  12.01   ; qtot 
0.6357
21 amber99_38  1DG5 N2 21 -0.923  14.01   ; qtot 
-0.2873
22 amber99_17  1DG5H21 22 0.4235  1.008   ; qtot 
0.1362
23 amber99_17  1DG5H22 23 0.4235  1.008   ; qtot 
0.5597
24 amber99_37  1DG5 N3 24-0.6636  14.01   ; qtot 
-0.1039
25  amber99_4  1DG5 C4 25 0.1814  12.01   ; qtot 
0.0775
26 amber99_11  1DG5C3' 26 0.0713  12.01   ; qtot 
0.1488
27 amber99_19  1DG5H3' 27 0.0985  1.008   ; qtot 
0.2473
28 amber99_11  1DG5C2' 28-0.0854  12.01   ; qtot 
0.1619
29 amber99_18  1DG5   H2'1 29 0.0718  1.008   ; qtot 
0.2337
30 amber99_18  1DG5   H2'2 30 0.0718  1.008   ; qtot 
0.3055
31 amber99_44  1DG5O3' 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

Re: [gmx-users] amber DNA non-integer charge

2011-08-28 Thread Justin A. Lemkul




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  1DG5H5T  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  1DG5O5'  1-0.6318 16   ; qtot 
-0.6318
 2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
-0.1896
 3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
-0.1965
 4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
-0.1211
 5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
-0.0457
 6 amber99_11  1DG5C4'  6 0.1629  12.01   ; qtot 
0.1172
 7 amber99_19  1DG5H4'  7 0.1176  1.008   ; qtot 
0.2348
 8 amber99_44  1DG5O4'  8-0.3691 16   ; qtot 
-0.1343
 9 amber99_11  1DG5C1'  9 0.0358  12.01   ; qtot 
-0.0985
10 amber99_20  1DG5H1' 10 0.1746  1.008   ; qtot 
0.0761
11 amber99_40  1DG5 N9 11 0.0577  14.01   ; qtot 
0.1338
12  amber99_6  1DG5 C8 12 0.0736  12.01   ; qtot 
0.2074
13 amber99_24  1DG5 H8 13 0.1997  1.008   ; qtot 
0.4071
14 amber99_36  1DG5 N7 14-0.5725  14.01   ; qtot 
-0.1654
15  amber99_4  1DG5 C5 15 0.1991  12.01   ; qtot 
0.0337
16  amber99_2  1DG5 C6 16 0.4918  12.01   ; qtot 
0.5255
17 amber99_41  1DG5 O6 17-0.5699 16   ; qtot 
-0.0444
18 amber99_35  1DG5 N1 18-0.5053  14.01   ; qtot 
-0.5497
19 amber99_25  1DG5 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  1DG5 C2 20 0.7432  12.01   ; qtot 
0.6357
21 amber99_38  1DG5 N2 21 -0.923  14.01   ; qtot 
-0.2873
22 amber99_17  1DG5H21 22 0.4235  1.008   ; qtot 
0.1362
23 amber99_17  1DG5H22 23 0.4235  1.008   ; qtot 
0.5597
24 amber99_37  1DG5 N3 24-0.6636  14.01   ; qtot 
-0.1039
25  amber99_4  1DG5 C4 25 0.1814  12.01   ; qtot 
0.0775
26 amber99_11  1DG5C3' 26 0.0713  12.01   ; qtot 
0.1488
27 amber99_19  1DG5H3' 27 0.0985  1.008   ; qtot 
0.2473
28 amber99_11  1DG5C2' 28-0.0854  12.01   ; qtot 
0.1619
29 amber99_18  1DG5   H2'1 29 0.0718  1.008   ; qtot 
0.2337
30 amber99_18  1DG5   H2'2 30 0.0718  1.008   ; qtot 
0.3055
31 amber99_44  1DG5O3' 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

RE: [gmx-users] amber DNA non-integer charge

2011-08-28 Thread Kamesh Narasimhan

I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are 
as you mentioned.

H1amber99_170.3520019

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  1DG5 H1 19   0.352001.008   ; 

is written by pdb2gmx as

amber99_25  1DG5 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  1DG5O5'  1-0.6318 16   ; qtot -0.6318
 2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
-0.1896
 3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
-0.1965
 4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
-0.1211
 5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
-0.0457
 6 amber99_11  1DG5C4'  6 0.1629  12.01   ; qtot 
0.1172
 7 amber99_19  1DG5H4'  7 0.1176  1.008   ; qtot 
0.2348
 8 amber99_44  1DG5O4'  8-0.3691 16   ; qtot 
-0.1343
 9 amber99_11  1DG5C1'  9 0.0358  12.01   ; qtot 
-0.0985
10 amber99_20  1DG5H1' 10 0.1746  1.008   ; qtot 
0.0761
11 amber99_40  1DG5 N9 11 0.0577  14.01   ; qtot 
0.1338
12  amber99_6  1DG5 C8 12 0.0736  12.01   ; qtot 
0.2074
13 amber99_24  1DG5 H8 13 0.1997  1.008   ; qtot 
0.4071
14 amber99_36  1DG5 N7 14-0.5725  14.01   ; qtot 
-0.1654
15  amber99_4  1DG5 C5 15 0.1991  12.01   ; qtot 
0.0337
16  amber99_2  1DG5 C6 16 0.4918  12.01   ; qtot 
0.5255
17 amber99_41  1DG5 O6 17-0.5699 16   ; qtot 
-0.0444
18 amber99_35  1DG5 N1 18-0.5053  14.01   ; qtot 
-0.5497
19 amber99_25  1DG5 H1 19 0.4422  1.008   ; qtot 
-0.1075
20  amber99_3  1DG5 C2 20 0.7432  12.01   ; qtot 
0.6357
21 amber99_38  1DG5 N2 21 -0.923  14.01   ; qtot 
-0.2873
22 amber99_17  1DG5H21 22 0.4235  1.008   ; qtot 
0.1362
23 amber99_17  1DG5H22 23 0.4235  1.008   ; qtot 
0.5597
24 amber99_37  1DG5 N3 24-0.6636  14.01   ; qtot 
-0.1039
25  amber99_4  1DG5 C4 25 0.1814  12.01   ; qtot 
0.0775
26 amber99_11  1DG5C3' 26 0.0713  12.01   ; qtot 
0.1488
27 amber99_19  1DG5H3' 27 0.0985  1.008   ; qtot 
0.2473
28 amber99_11  1DG5C2' 28-0.0854  12.01   ; qtot 
0.1619
29 amber99_18  1DG5   H2'1 29 0.0718  1.008   ; qtot 
0.2337
30 amber99_18  1DG5   H2'2 30 0.0718  1.008   ; qtot 
0.3055
31 amber99_44  1DG5O3' 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  1DG5H5T  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  1DG5O5'  1-0.6318 16   ; qtot 
 -0.6318
  2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
 -0.1896
  3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
 -0.1965
  4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
 -0.1211
  5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
 -0.0457
  6 amber99_11  1

Re: [gmx-users] amber DNA non-integer charge

2011-08-28 Thread Justin A. Lemkul




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.

H1amber99_170.3520019

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  1DG5 H1 19   0.352001.008   ; 


is written by pdb2gmx as

amber99_25  1DG5 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  1DG5O5'  1-0.6318 16   ; qtot -0.6318
 2 amber99_25  1DG5H5T  2 0.4422  1.008   ; qtot 
-0.1896
 3 amber99_11  1DG5C5'  3-0.0069  12.01   ; qtot 
-0.1965
 4 amber99_19  1DG5   H5'1  4 0.0754  1.008   ; qtot 
-0.1211
 5 amber99_19  1DG5   H5'2  5 0.0754  1.008   ; qtot 
-0.0457
 6 amber99_11  1DG5C4'  6 0.1629  12.01   ; qtot 
0.1172
 7 amber99_19  1DG5H4'  7 0.1176  1.008   ; qtot 
0.2348
 8 amber99_44  1DG5O4'  8-0.3691 16   ; qtot 
-0.1343
 9 amber99_11  1DG5C1'  9 0.0358  12.01   ; qtot 
-0.0985
10 amber99_20  1DG5H1' 10 0.1746  1.008   ; qtot 
0.0761
11 amber99_40  1DG5 N9 11 0.0577  14.01   ; qtot 
0.1338
12  amber99_6  1DG5 C8 12 0.0736  12.01   ; qtot 
0.2074
13 amber99_24  1DG5 H8 13 0.1997  1.008   ; qtot 
0.4071
14 amber99_36  1DG5 N7 14-0.5725  14.01   ; qtot 
-0.1654
15  amber99_4  1DG5 C5 15 0.1991  12.01   ; qtot 
0.0337
16  amber99_2  1DG5 C6 16 0.4918  12.01   ; qtot 
0.5255
17 amber99_41  1DG5 O6 17-0.5699 16   ; qtot 
-0.0444
18 amber99_35  1DG5 N1 18-0.5053  14.01   ; qtot 
-0.5497
19 amber99_25  1DG5 H1 19 0.4422  1.008   ; qtot 
-0.1075
20  amber99_3  1DG5 C2 20 0.7432  12.01   ; qtot 
0.6357
21 amber99_38  1DG5 N2 21 -0.923  14.01   ; qtot 
-0.2873
22 amber99_17  1DG5H21 22 0.4235  1.008   ; qtot 
0.1362
23 amber99_17  1DG5H22 23 0.4235  1.008   ; qtot 
0.5597
24 amber99_37  1DG5 N3 24-0.6636  14.01   ; qtot 
-0.1039
25  amber99_4  1DG5 C4 25 0.1814  12.01   ; qtot 
0.0775
26 amber99_11  1DG5C3' 26 0.0713  12.01   ; qtot 
0.1488
27 amber99_19  1DG5H3' 27 0.0985  1.008   ; qtot 
0.2473
28 amber99_11  1DG5C2' 28-0.0854  12.01   ; qtot 
0.1619
29 amber99_18  1DG5   H2'1 29 0.0718  1.008   ; qtot 
0.2337
30 amber99_18  1DG5   H2'2 30 0.0718  1.008   ; qtot 
0.3055
31 amber99_44  1DG5O3' 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  1DG5H5T  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  1DG5O5'  1-0.6318 16   ; qtot 
-0.6318
 2 amber99_25  1DG5H5T

RE: [gmx-users] amber DNA non-integer charge

RE: [gmx-users] amber DNA non-integer charge

Re: [gmx-users] amber DNA non-integer charge

RE: [gmx-users] amber DNA non-integer charge

Re: [gmx-users] amber DNA non-integer charge

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