[gmx-users] How to cap a single residue in gromacs (Alessandra Villa)
Sadaf Rani
sadafrani6 at gmail.com
Wed Feb 19 12:29:36 CET 2020
Thank you, Alessandra, for your reply.
I have tried TER in the PDB file but it doesn't work. It requires an N and
C terminal for amino acid residue. I have prepared residue in avogadros and
used these coordinates.
ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00
N1+
ATOM 2 CA PHE A 1 1.462 0.000 0.000 1.00 0.00
C
ATOM 3 C PHE A 1 1.902 0.000 1.473 1.00 0.00
C
ATOM 4 O PHE A 1 1.105 0.000 2.411 1.00 0.00
O
ATOM 5 CB PHE A 1 2.020 1.225 -0.743 1.00 0.00
C
ATOM 6 CG PHE A 1 3.442 1.037 -1.219 1.00 0.00
C
ATOM 7 CD2 PHE A 1 4.512 1.642 -0.547 1.00 0.00
C
ATOM 8 CE2 PHE A 1 5.823 1.440 -0.982 1.00 0.00
C
ATOM 9 CZ PHE A 1 6.074 0.642 -2.097 1.00 0.00
C
ATOM 10 CE1 PHE A 1 5.015 0.044 -2.777 1.00 0.00
C
ATOM 11 CD1 PHE A 1 3.705 0.238 -2.340 1.00 0.00
C
ATOM 12 H PHE A 1 -0.467 0.280 0.859 1.00 0.00
H
ATOM 13 HA PHE A 1 1.790 -0.939 -0.463 1.00 0.00
H
ATOM 14 HB1 PHE A 1 1.956 2.118 -0.106 1.00 0.00
H
ATOM 15 HB2 PHE A 1 1.405 1.454 -1.623 1.00 0.00
H
ATOM 16 HD2 PHE A 1 4.334 2.273 0.322 1.00 0.00
H
ATOM 17 HE2 PHE A 1 6.649 1.912 -0.456 1.00 0.00
H
ATOM 18 HZ PHE A 1 7.094 0.492 -2.441 1.00 0.00
H
ATOM 19 HE1 PHE A 1 5.208 -0.570 -3.654 1.00 0.00
H
ATOM 20 HD1 PHE A 1 2.885 -0.231 -2.885 1.00 0.00
H
ATOM 21 HN PHE A 1 -0.339 0.853 -0.435 1.00 0.00
H
ATOM 22 2HN PHE A 1 -0.339 -0.853 -0.435 1.00 0.00
H
ATOM 23 OXT PHE A 1 3.231 -0.000 1.717 1.00 0.00
O1-
However, it claims that in the chosen force field there is no residue type
for 'PHE' as a standalone
(starting & ending) residue
I am using AMBER99SB-ILDN force field for protein.
I have looked into the force field both CPHE and NPHE are different as
below:-
[ CPHE ]
[ atoms ]
N N -0.38210 1
H H 0.26810 2
CA CT -0.18250 3
HA H1 0.10980 4
CB CT -0.09590 5
HB1 HC 0.04430 6
HB2 HC 0.04430 7
CG CA 0.05520 8
CD1 CA -0.13000 9
HD1 HA 0.14080 10
CE1 CA -0.18470 11
HE1 HA 0.14610 12
CZ CA -0.09440 13
HZ HA 0.12800 14
CE2 CA -0.18470 15
HE2 HA 0.14610 16
CD2 CA -0.13000 17
HD2 HA 0.14080 18
C C 0.76600 19
OC1 O2 -0.80260 20
OC2 O2 -0.80260 21
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ HZ
CZ CE2
CE2 HE2
CE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ impropers ]
-C CA N H
CA OC1 C OC2
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CE1 CE2 CZ HZ
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
[ NPHE ]
[ atoms ]
N N3 0.17370 1
H1 H 0.19210 2
H2 H 0.19210 3
H3 H 0.19210 4
CA CT 0.07330 5
HA HP 0.10410 6
CB CT 0.03300 7
HB1 HC 0.01040 8
HB2 HC 0.01040 9
CG CA 0.00310 10
CD1 CA -0.13920 11
HD1 HA 0.13740 12
CE1 CA -0.16020 13
HE1 HA 0.14330 14
CZ CA -0.12080 15
HZ HA 0.13290 16
CE2 CA -0.16030 17
HE2 HA 0.14330 18
CD2 CA -0.13910 19
HD2 HA 0.13740 20
C C 0.61230 21
O O -0.57130 22
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ HZ
CZ CE2
CE2 HE2
CE2 CD2
CD2 HD2
C O
C +N
[ impropers ]
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CE1 CE2 CZ HZ
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
How should I build it.
Thanks.
Sadaf
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