Adding residues in GROMACS

houghb edited this page Feb 4, 2016 · 1 revision

Steps

edit aminoacids.rtp file

take a look at the AAs that are present, the format is fairly straight forward. You can look inside ffbonded to make sure you properly label each atom (these vary depending on bonded neighbors).

edit aminoacids.hdb

The number next to the residue name denotes how many lines GROMACS needs to read for that residue The number in the first column denotes the amount of H’s GROMACS needs to add The number in the second column is bond-type specific and ranges 1-6 The order of appearance in the file is important. GROMACS reads from the N-linking/N-terminal H’s (one or the other) to the C-alpha H’s (if present), down the side chain, then the C-terminal carboxyl group (if present).

tips

A subtlety that can cause you trouble is that All H’s in the .gro file need to be unique to a given molecule/protein. So if the residue you add in the .rtp file has repeating units, make each atom in the individual units distinct with their lettering scheme. If this issue occurs you will see your H’s flying off your monomers/residues during energy minimization

For the [1 1] .hdb hydrogen add, GROMACS does not number this hydrogen since there is only one of them. So match the nomenclature for this atom exactly between the .hdb and .rtp files.

See my example 7-monomer poly-ethylene glycol at the end of the post.

examples

    1       1
for N-linking N-H bonds, C-terminal O-H bonds, aromatic C-H bonds
ex:
    1       1       H       N       -C      CA 	#SER
    1       1       OC1     C       CA      OC2 	#CSER, note: carboxyl group without H
    1       1       HE2     CE2     CZ      CD2	#TYR
    1       2
for sidechain O-H bonds
ex:
    1       2       HG      OG      CB      CA 	#SER
    1       5
for C-alpha C-H bonds, SP3 Carbons with 1 H
ex:
    1       5       HA      CA      N       CB      C	#SER
    1       5       HB      CB      CA      CG2     OG1	#THR
    2       3
for N-H2 bonds
ex:
    2       3       HH1     NH1     CZ      NE	#ARG
    2       6
for alkane chains
ex:
    2       6       HB      CB      CA      CG	#LYS
    3        4
for N-terminal N-H3 bonds, SP3 C-H3 bonds
ex:
    3       4       H       N       CA      CB	#NSER
    3       4       HG2     CG2     CB      CA	#THR
rtp

[ 7EG ] [ atoms ] CC1 CT -0.0971 1 HA1 H1 0.0487 2 HA2 H1 0.0487 3 HA3 H1 0.0407 4 CC2 CT 0.1324 5 HB1 H1 0.0257 6 HB2 H1 0.0257 7 OC1 OS -0.4286 8 C1 CT 0.1292 9 HC1 H1 0.0405 10 HC2 H1 0.0405 11 C2 CT 0.1322 12 HD1 H1 0.0445 13 HD2 H1 0.0445 14 O1 OS -0.4316 15 C3 CT 0.1292 16 HE1 H1 0.0405 17 HE2 H1 0.0405 10 C4 CT 0.1322 18 HF1 H1 0.0445 19 HF2 H1 0.0445 20 O2 OS -0.4316 21 C5 CT 0.1292 22 HG1 H1 0.0405 23 HG2 H1 0.0405 24 C6 CT 0.1322 25 HH1 H1 0.0445 26 HH2 H1 0.0445 27 O3 OS -0.4316 28 C7 CT 0.1292 29 HI1 H1 0.0405 30 HI2 H1 0.0405 31 C8 CT 0.1322 32 HJ1 H1 0.0445 33 HJ2 H1 0.0445 34 O4 OS -0.4316 35 C9 CT 0.1292 36 HK1 H1 0.0405 37 HK2 H1 0.0405 38 C10 CT 0.1322 39 HL1 H1 0.0445 40 HL2 H1 0.0445 41 O5 OS -0.4316 42 CO1 CT 0.1228 43 HM1 H1 0.0405 44 HM2 H1 0.0405 45 CO2 CT 0.1209 46 HN1 H1 0.0339 47 HN2 H1 0.0339 48 OO1 OH -0.5729 49 HO1 HO 0.3843 50 [ bonds ] CC1 HA1 CC1 HA2 CC1 HA3 CC2 CC1 CC2 HB1 CC2 HB2 OC1 CC2 C1 OC1 C1 HC1 C1 HC2 C2 C1 C2 HD1 C2 HD2 O1 C2 C3 O1 C3 HE1 C3 HE2 C4 C3 C4 HF1 C4 HF2 O2 C4 C5 O2 C5 HG1 C5 HG2 C6 C5 C6 HH1 C6 HH2 O3 C6 C7 O3 C7 HI1 C7 HI2 C8 C7 C8 HJ1 C8 HJ2 O4 C8 C9 O4 C9 HK1 C9 HK2 C10 C9 C10 HL1 C10 HL2 O5 C10 CO1 O5 CO1 HM1 CO1 HM2 CO2 CO1 CO2 HN1 CO2 HN2 OO1 CO2 HO1 OO1

hdb
7EG    15
3       4       HA      CC1     CC2     OC1
2       6       HB      CC2     CC1     OC1
2       6       HC      C1      OC1     C2
2       6       HD      C2      C1      O1
2       6       HE      C3      O1      C4
2       6       HF      C4      C3      O2
2       6       HG      C5      O2      C6
2       6       HH      C6      C5      O3
2       6       HI      C7      O3      C8
2       6       HJ      C8      C7      O4
2       6       HK      C9      O4      C10
2       6       HL      C10     C9      O5
2       6       HM      CO1     O5      CO2
2       6       HN      CO2     CO1     OO1
1       1       HO1     OO1     CO2     CO1
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.