Problem using pdb2gmx with newly added PNA residues

GROMACS version: 2019.3
GROMACS modification: Yes/No
Here post your question

Hello everyone!

I’m trying to use pdb2gmx on peptide nucleic acid (PNA) residues in Amber99sb forcefield,
but it doesn’t seem to recognize it as a single chain and I just want to know what I’m doing wrong here.

To start off, I wrote a new rtp file (pna.rtp). The atom types and the partial charges were obtained from the website (http://upjv.q4md-forcefieldtools.org/RED/). To match the rtp format to that of other nucleic acids (DNA/RNA), I also added the C-ter and N-ter residues. Here’s the example output of my rtp file:

[ NAPN ] ; N-ter Adenosine PNA
[ atoms ]
N1’ N3 0.00490 1
H1’1 H 0.25310 2
H1’2 H 0.25310 3
H1’3 H 0.25310 4
C2’ CT 0.07230 5
H2’1 HP 0.08190 6
H2’2 HP 0.08190 7
C3’ CT -0.06060 8
H3’1 H1 0.08940 9
H3’2 H1 0.08940 10
N4’ N -0.06150 11
C5’ CT -0.12510 12
H5’1 H1 0.06740 13
H5’2 H1 0.06740 14
C’ C 0.61400 15
O1’ O -0.57540 16
C7’ C 0.45000 17
O7’ O -0.55980 18
C8’ CT -0.10550 19
H8’1 H1 0.11290 20
H8’2 H1 0.11290 21
N9 N* -0.08080 22
C8 CK 0.14310 23
H8 H5 0.16510 24
N7 NB -0.56260 25
C6 CA 0.65590 26
N6 N2 -0.88520 27
HN61 H 0.40410 28
HN62 H 0.40410 29
C5 CB 0.03620 30
C4 CB 0.43570 31
N3 NC -0.71750 32
C2 CQ 0.57280 33
H2 H5 0.05490 34
N1 NC -0.74160 35
[ bonds ]
N1’ H1’1
N1’ H1’2
N1’ H1’3
N1’ C2’
C2’ H2’1
C2’ H2’2
C2’ C3’
C3’ H3’1
C3’ H3’2
C3’ N4’
N4’ C5’
N4’ C7’
C5’ H5’1
C5’ H5’2
C5’ C’
C’ O1’
C7’ O7’
C7’ C8’
C8’ H8’1
C8’ H8’2
C8’ N9
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C6 N6
C6 C5
C6 N1
N6 HN61
N6 HN62
C5 C4
C4 N3
N3 C2
C2 H2
C2 N1
[ impropers ]
C4 C8 N9 C8’
C6 HN61 N6 HN62
N9 N7 C8 H8
N1 N3 C2 H2
C5 N6 C6 N1
[ APN ] ; Adenosie PNA
[ atoms ]
N1’ N -0.40300 1
H1’1 H 0.28420 2
C2’ CT -0.12410 3
H2’1 H1 0.11470 4
H2’2 H1 0.11470 5
C3’ CT -0.05220 6
H3’1 H1 0.10330 7
H3’2 H1 0.10330 8
N4’ N -0.09410 9
C5’ CT -0.11120 10
H5’1 H1 0.06780 11
H5’2 H1 0.06780 12
C’ C 0.62090 13
O1’ O -0.58070 14
C7’ C 0.43910 15
O7’ O -0.55020 16
C8’ CT -0.12140 17
H8’1 H1 0.11240 18
H8’2 H1 0.11240 19
N9 N* -0.05780 20
C8 CK 0.12980 21
H8 H5 0.16770 22
N7 NB -0.55820 23
C6 CA 0.65970 24
N6 N2 -0.88830 25
HN61 H 0.40480 26
HN62 H 0.40480 27
C5 CB 0.03000 28
C4 CB 0.43430 29
N3 NC -0.71270 30
C2 CQ 0.56600 31
H2 H5 0.05600 32
N1 NC -0.73980 33
[ bonds ]
N1’ H1’1
N1’ C2’
C2’ H2’1
C2’ H2’2
C2’ C3’
C3’ H3’1
C3’ H3’2
C3’ N4’
N4’ C5’
N4’ C7’
C5’ H5’1
C5’ H5’2
C5’ C’
C’ O1’
C7’ O7’
C7’ C8’
C8’ H8’1
C8’ H8’2
C8’ N9
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C6 N6
C6 C5
C6 N1
N6 HN61
N6 HN62
C5 C4
C4 N3
N3 C2
C2 H2
C2 N1
[ impropers ]
C4 C8 N9 C8’
C6 HN61 N6 HN62
N9 N7 C8 H8
N1 N3 C2 H2
C5 N6 C6 N1

I also wrote the hydrogen database (pna.hdb) file, residue to building block file (pna.r2b), and the file (pna.arn)