Hi Gromacs users,
I have a 65 amino-acid protein chain where I added acetyl and amide capping groups to the N- and C-termini, respectively.I want to add a pseudo-amino acid (called ANX) instead of amino acid 61 (ASN61). To be able to do this, according to the link below, I made the following changes:
1- I made a copy of gromos54a7 force field directory into my working directory.
2- I added the new residue (ANX) to the .rtp file for the force field I chose.
[ ANX ]
[ atoms ]
N N 0.03695 0
CA CH1 0.02889 1
CB CH2 0.05414 1
CG C 0.22287 2
OD1 O -0.25244 2
ND2 NT -0.20901 2
CD CH1 0.34145 3
CE CH1 0.02370 4
NE2 N -0.08297 5
CP CH1 0.20036 6
OP1 OA -0.27220 6
CQ CH3 0.07359 7
CZ CH1 0.16236 8
OZ1 OA -0.29272 8
CM CH1 0.22151 9
OM1 OA -0.29572 9
CN CH1 0.11181 10
CO CH2 0.28394 10
OO1 OA -0.20218 10
OD2 OA -0.21004 11
C C 0.22546 12
O O -0.16973 12
and with [bonds], [angles], [impropers] and [dihedral] sections.
3- I added my residue to residuetypes.dat as: ANX Protein
4- I updated the specbond.dat to make a connectivity of ANX residue to the previous residue and the residue after it.
( SER C 1 ANX N 1 1.34 SER2 ANX1 and
VAL N 1 ANX C 1 1.35 VAL1 ANX1 )
Ps. I didn’t make any changes in the the atomtypes.atp, ffnonbonded.itp and ffbonded.itp; because there are no new atom types or new bonded types.
5- When I use the pdb2gmx command with –ter flag, I get the following:
1: Select start terminus type for ACE-1
(I choose “None”)
2: Select end terminus type for SER-60:
(So; it does not see my new residue (ANX) that is number 61; and it tries to add a terminus to the residue 60 that is previous of ANX. I was expecting to get the following:
Select end terminus type for NH2-66
It seems that gromacs does not see the new residue I added to the force field.
Any help would be appreciated.