Have you looked in the ffnabonded.itp and ffnanonbonded.itp? To me it
looks like all of the atom types/bonds/angles are there.
I have just made a very quick rtp entry from the stream file (see
attached) and it seems to work fine (but please do check it). Note the
very large charge groups, so you should use the -nochargegrp option of
pdb2gmx.
Cheers
Tom
David Parcej wrote:
Hi all,
Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The
forcefield files are missing atom and bond types and angle information.
This is available for charmm, but I have only found it in "stream" file
and have no idea how to convert it. It should be possible (for someone
smarter than me).
cheers
Dave
--
Dr Thomas Piggot
University of Southampton, UK.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 5 9 2 1 3 1 0
[ATP]
;
; from toppar_all27_na_nad_ppi.str. Thomas Piggot 17/9/10
;
[atoms]
C4' CN7 0.16 0
H4' HN7 0.09 0
O4' ON6B -0.50 0
C1' CN7B 0.16 0
H1' HN7 0.09 0
C5 CN5 0.28 1
N7 NN4 -0.71 1
C8 CN4 0.34 1
H8 HN3 0.12 1
N9 NN2 -0.05 1
N1 NN3A -0.74 2
C2 CN4 0.50 2
H2 HN3 0.13 2
N3 NN3A -0.75 2
C4 CN5 0.43 2
C6 CN2 0.46 2
N6 NN1 -0.77 3
H61 HN1 0.38 3
H62 HN1 0.38 3
C2' CN7B 0.14 4
H2'' HN7 0.09 4
O2' ON5 -0.66 4
H2' HN5 0.43 4
C3' CN7 0.14 5
H3' HN7 0.09 5
O3' ON5 -0.66 5
H3T HN5 0.43 5
C5' CN8B -0.08 6
H5' HN8 0.09 6
H5'' HN8 0.09 6
O5' ON2 -0.62 6
PA P 1.50 6
O1A ON3 -0.82 6
O2A ON3 -0.82 6
O3A ON2 -0.74 6
PB P2 1.50 6
O1B ON3 -0.82 6
O2B ON3 -0.82 6
O3B ON2 -0.86 6
PG P2 1.10 6
O1G ON3 -0.90 6
O2G ON3 -0.90 6
O3G ON3 -0.90 6
[bonds]
O5' C5'
O5' PA
PA O1A
PA O2A
PA O3A
O3A PB
PB O1B
PB O2B
PB O3B
O3B PG
PG O1G
PG O2G
PG O3G
C5' C4'
C4' O4'
C4' C3'
O4' C1'
C1' N9
C1' C2'
N9 C4
N9 C8
C4 N3
C2 N1
C6 N6
N6 H61
N6 H62
C6 C5
C5 N7
C2' C3'
C2' O2'
O2' H2'
C3' O3'
O3' H3T
C1' H1'
C2' H2''
C3' H3'
C4' H4'
C5' H5'
C5' H5''
C8 H8
C2 H2
N1 C6
N3 C2
C4 C5
N7 C8
[impropers]
N6 C6 H61 H62
C6 N1 C5 N6
--
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