http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

You need to create an .rtp entry for a custom residue that contains the amino acid linked to the covalent adduct. Do not use PRODRG parameters; they are of insufficient quality for MD simulations without significant refinement. Moreover, PRODRG is to be used only with GROMOS parameter sets, not any of those you have listed above.

Dear Justin,

Many more thanks but could you give me any example for step by step .rtp file creation.

Thanking you in advance

The file format is described in the GROMACS manual, Chapter 5. All you're doing is modifying an existing amino acid to create a new residue, so copy the contents of that amino acid into a newly named residue definition and modify as needed.

Dear Justin,

This is my modeled structure

LINK C1 BGC A 505 OD2 ASP A 192 1555 1555 1.49

ATOM 1 N MET A 1 24.302 64.094 -59.895 1.00 25.08 N

ATOM 2 CA MET A 1 25.597 64.337 -59.199 1.00 22.91 C

ATOM 3 C MET A 1 26.726 64.293 -60.221 1.00 22.81 C

ATOM 4 O MET A 1 26.804 63.351 -61.014 1.00 23.00 O

ATOM 5 CB MET A 1 25.810 63.286 -58.091 1.00 22.78 C

ATOM 6 CG MET A 1 26.934 63.614 -57.110 1.00 21.69 C

ATOM 7 SD MET A 1 27.096 62.493 -55.701 1.00 21.64 S

ATOM 8 CE MET A 1 25.612 62.862 -54.789 1.00 20.43 C

.

.

ATOM 1536 N ASP A 192 21.763 61.500 -42.930 1.00 23.26 N

ATOM 1537 CA ASP A 192 22.450 60.760 -41.874 1.00 23.10 C

ATOM 1538 C ASP A 192 21.481 59.958 -41.016 1.00 23.23 C

ATOM 1539 O ASP A 192 20.419 60.457 -40.621 1.00 22.22 O

ATOM 1540 CB ASP A 192 23.284 61.722 -41.002 1.00 25.40 C

ATOM 1541 CG ASP A 192 23.930 61.035 -39.785 1.00 27.69 C

ATOM 1542 OD1 ASP A 192 23.418 61.230 -38.655 1.00 29.53 O

ATOM 1543 OD2 ASP A 192 25.098 60.228 -39.969 1.00 28.06 O1-

.

.

ATOM 3960 N ALA A 504 46.284 63.907 -71.577 1.00 35.11 N

ATOM 3961 CA ALA A 504 46.855 64.837 -72.555 1.00 37.20 C

ATOM 3962 C ALA A 504 46.040 66.119 -72.719 1.00 38.54 C

ATOM 3963 O ALA A 504 44.802 66.020 -72.846 1.00 40.48 O

ATOM 3964 CB ALA A 504 47.008 64.143 -73.892 1.00 35.72 C

ATOM 3965 OXT ALA A 504 46.654 67.208 -72.691 1.00 41.98 O1-

TER 3966 ALA A 504

HETATM 3967 C2 BGC A 505 27.366 59.540 -39.061 1.00 28.08 C

HETATM 3968 C3 BGC A 505 28.063 59.219 -37.697 1.00 28.15 C

HETATM 3969 C4 BGC A 505 27.184 59.603 -36.510 1.00 27.68 C

HETATM 3970 C5 BGC A 505 25.841 58.850 -36.553 1.00 27.24 C

HETATM 3971 C6 BGC A 505 24.729 59.619 -35.854 1.00 29.21 C

HETATM 3972 C1 BGC A 505 25.810 59.270 -39.070 1.00 30.28 C

HETATM 3973 O2 BGC A 505 28.005 58.761 -40.050 1.00 29.46 O

HETATM 3974 O3 BGC A 505 29.303 59.931 -37.597 1.00 24.50 O

HETATM 3975 O4 BGC A 505 27.858 59.293 -35.303 1.00 23.23 O

HETATM 3976 O5 BGC A 505 25.364 58.473 -37.919 1.00 30.31 O

HETATM 3977 O6 BGC A 505 24.636 60.976 -36.259 1.00 29.14 O

CONECT 1543 3972

CONECT 3967 3968 3972 3973

CONECT 3968 3967 3969 3974

CONECT 3969 3968 3970 3975

CONECT 3970 3969 3971 3976

CONECT 3971 3970 3977

CONECT 3972 1543 3967 3976

CONECT 3973 3967

CONECT 3974 3968

CONECT 3975 3969

CONECT 3976 3970 3972

CONECT 3977 3971

END

1. As you said i have included ligand (B-D-glucose) in aminoacid.rtp file

[ BGC ]

[ atoms ]

C4 CH1R 0.23200 1

O4 OA -0.64200 1

HO4 H 0.41000 1

C3 CH1R 0.23200 2

O3 OA -0.64200 2

HO3 H 0.41000 2

C2 CH1R 0.23200 3

O2 OA -0.64200 3

HO2 H 0.41000 3

C6 CH2 0.23200 4

O6 OA -0.64200 4

HO6 H 0.41000 4

C5 CH1R 0.23200 5

O5 OR -0.46400 5

C1 CH1R 0.46400 5

O1 OA -0.64200 5

HO1 H 0.41000 5

[ bonds ]

HO4 O4 gb_1

O2 HO2 gb_1

O3 HO3 gb_1

O6 HO6 gb_1

O1 HO1 gb_1

O4 C4 gb_20

C4 C3 gb_26

C4 C5 gb_26

C2 O2 gb_20

C2 C3 gb_26

C2 C1 gb_26

C3 O3 gb_20

C6 O6 gb_20

C6 C5 gb_26

C5 O5 gb_20

O5 C1 gb_20

C1 O1 gb_20

[ angles ]

; ai aj ak gromos type

HO4 O4 C4 ga_12

C2 O2 HO2 ga_12

C3 O3 HO3 ga_12

C6 O6 HO6 ga_12

C1 O1 HO1 ga_12

O4 C4 C3 ga_9

O4 C4 C5 ga_9

C3 C4 C5 ga_8

O2 C2 C3 ga_9

O2 C2 C1 ga_9

C3 C2 C1 ga_8

C4 C3 C2 ga_8

C4 C3 O3 ga_9

C2 C3 O3 ga_9

O6 C6 C5 ga_9

C4 C5 C6 ga_8

C4 C5 O5 ga_9

C6 C5 O5 ga_9

C5 O5 C1 ga_10

C2 C1 O5 ga_9

C2 C1 O1 ga_9

O5 C1 O1 ga_9

[ impropers ]

; ai aj ak al gromos type

C2 C3 C1 O2 gi_2

C3 C2 C4 O3 gi_2

O4 C3 C5 C4 gi_2

C5 C4 O5 C6 gi_2

O1 C2 O5 C1 gi_2

[ dihedrals ]

; ai aj ak al gromos type

HO2 O2 C2 C1 gdc_t3 ; [T3: X-C-O-H (generic hydroxyl)]

C2 C3 O3 HO3 gdc_t3 ; [T3: X-C-O-H (generic hydroxyl)]

C3 C4 O4 HO4 gdc_t3 ; [T3: X-C-O-H (generic hydroxyl)]

C5 C6 O6 HO6 gdc_t3 ; [T3: X-C-O-H (generic hydroxyl)]

O5 C1 O1 HO1 gdc_t3 ; [T3: X-C-O-H (generic hydroxyl)]

O5 C1 O1 HO1 gdc_t4 ; [T4: Or-CH*r-O-X (exo-anomeric)]

O2 C2 C3 O3 gdc_t12; [T12: Ox-X-X-Ox; not type T13(oxygen-oxygen gauche)]

C1 C2 C3 C4 gdc_t1 ; [T1: X-C-C-X; X not H (generic CC -unaltered from 53A6)]

O2 C2 C1 O5 gdc_t13; [T13: Ox-X-X-Or (oxygen-oxygenintracyclic)]

O2 C2 C1 O1 gdc_t12; [T12: Ox-X-X-Ox; not type T13(oxygen-oxygen gauche)]

C3 C2 C1 O5 gdc_t1 ; [T1: X-C-C-X; X not H (generic CC -unaltered from 53A6)]

C2 C3 C4 C5 gdc_t1 ; [T1: X-C-C-X; X not H (generic CC -unaltered from 53A6)]

O3 C3 C4 O4 gdc_t12; [T12: Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche)]

C3 C4 C5 O5 gdc_t1 ; [T1: X-C-C-X; X not H (generic CC -unaltered from 53A6)]

O4 C4 C5 O5 gdc_t13; [T13: Ox-X-X-Or (oxygen-oxygenintracyclic)]

O6 C6 C5 C4 gdc_t1 ; [T1: X-C-C-X; X not H (generic CC -unaltered from 53A6)]

O6 C6 C5 C4 gdc_t10; [T10: Xr-CH*r-CH*-O (exocyclicoxymethyl)]

O6 C6 C5 O5 gdc_t11; [T11: Xr-CH*r-CH*-O (exocyclicoxymethyl)]

O6 C6 C5 O5 gdc_t12; [T12: Ox-X-X-Ox; not type T13(oxygen-oxygen gauche)]

C4 C5 O5 C1 gdc_t2 ; [T2: X-C-O-X; X not H (generic CO)]

C5 O5 C1 C2 gdc_t2 ; [T2: X-C-O-X; X not H (generic CO)]

C5 O5 C1 O1 gdc_t5 ; [T5: CH*r-Or-CH*r-O (anomeric)]

[ exclusions ]

C6 O1

C6 O3

HO1 C5

HO1 C3

HO2 C4

HO2 O5

HO3 C1

HO3 C5

HO4 C2

HO4 O5

2. I have added covalent link details in specbond.dat

11

ASP OD2 1 BGC C1 1 1.49 ASP BGC

BGC C1 1 ASP OD2 1 1.49 BGC ASP

BGC C2 1 BGC O5 1 1.49 BGC BGC

CYS SG 1 CYS SG 1 0.2 CYS2 CYS2

CYS SG 1 HEM FE 2 0.25 CYS2 HEME

CYS SG 1 HEM CAB 1 0.18 CYS2 HEME

CYS SG 1 HEM CAC 1 0.18 CYS2 HEME

HIS NE2 1 HEM FE 1 0.2 HIS1 HEME

MET SD 1 HEM FE 1 0.24 MET HEME

CO C 1 HEME FE 1 0.19 CO HEME

CYM SG 1 CYM SG 1 0.2 CYS2 CYS2

3. I have added h atom in aminoacids.hdb

BGC 4

1 2 HO2 O2 C2 C3

1 2 HO3 O3 C3 C2

1 2 HO4 O4 C4 C5

1 2 HO6 O6 C6 C5

after all this modification i can able to run successfully but there is no ligand either covalent in minimized structure.

May I know what are all the possible reasons for the same?

Thanking you in advance

Your example is a non-covalent ligand, so the story keeps changing here. The approach outlined in your last reply is for a non-covalent ligand, which is a different approach entirely. As for the last question, things can't magically disappear. Either the species is present in the coordinates and topology or it is not.

Dear Justin,

Thanks and i will consider your suggestion to do find a correct approach to do it.

Dear Justin,

As per your suggestion i have made the new residue topology .

But, started with an another issue with the following error:

Fatal error:

Atom OXT in residue ALA 504 was not found in rtp entry ALA with 6 atoms

while sorting atoms.

Normally, this should not happen because the terminal residue of the chain must have an OXT atom and this wont be provided either in .rtp file or atomtypes.dat. So, I don't know why i am getting this issue still i am working on the same but at the same time if i delete the OXT from the coordinate like below i can able to run successfully by linking the ligand and residue.

ATOM 3965 OXT ALA A 504 46.654 67.208 -72.691 1.00 41.98 O1-

TER 3966 ALA A 504

HETATM 3967 C2 BGC A 505 27.366 59.540 -39.061 1.00 28.08 C

TO

TER 3966 ALA A 504

HETATM 3967 C2 BGC A 505 27.366 59.540 -39.061 1.00 28.08 C

and in case of success run i get a message like below:

Before cleaning: 28 dihedrals

Making cmap torsions...There are 18 dihedrals, 4 impropers, 19 angles

23 pairs, 15 bonds and 0 virtual sites

Total mass 163.151 a.m.u.

Total charge 0.232 e

Writing topology

Including chain 1 in system: 5080 atoms 504 residues

Including chain 2 in system: 15 atoms 1 residues

Now there are 5095 atoms and 505 residues

Total mass in system 56327.123 a.m.u.

Total charge in system -25.078 e

Kindly give me suggestion about Atom OXT in residue ALA 504 was not found in rtp entry

Thanking you in advance