[gmx-users] How to cap a single residue in gromacs (Alessandra Villa)
Justin Lemkul
jalemkul at vt.edu
Thu Feb 20 16:39:55 CET 2020
On 2/19/20 6:29 AM, Sadaf Rani wrote:
> 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.
If you're trying to simulate a zwitterionic Phe residue, the AMBER force
field (at least, as implemented in GROMACS) does not support such a
species. If you want to cap it with acetyl and amide caps, you will need
to build those entities yourself and specify them as separate residues
(ACE and NME).
-Justin
--
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Justin A. Lemkul, Ph.D.
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