Fluorescent Dyes Force Fields

Using dyes in MD simulations, are useful in comparing for comparing computational results with experimental results. These dyes (technically fluorescent ligands) are used to study protein dynamics, such as folding and dissociation. The table below shows the dyes currently covered by AMBER.

Dye	Residue name	Linker residue
Alexa Fluor 350	A35	C1R, L1R
Alexa Fluor 488	A48	B1R,C1R, L1R
Alexa Fluor 532	A53	C1R, L1R
Alexa Fluor 568	A56	C1R, L1R
Alexa Fluor 594	A59	C1R, L1R
Alexa Fluor 647	A64	B1R,C2R, L1R
Lumiprope Cy3	C3N	C2R, L1R
Lumiprope Sulfo-Cy3	C3W	L1R
Lumiprope Cy5	C5N	C2R, L1R
Lumiprope Sulfo-Cy5	C5W	L1R
Lumiprope Cy5.5	C55	C2R, L1R
Lumiprope Cy7	C7N	L1R
Lumiprope Cy7.5	C75	L1R
ATTO 390	T39	C2R, L1R
ATTO 425	T42	C2R, L1R
ATTO 465	T46	C2R, L1R
ATTO 488	T48	C3R, L2R
ATTO 495	T49	C2R, L1R
ATTO 514	T51	C3R, L2R
ATTO 520	T52	C2R, L1R
ATTO 610	T61	C2R, L1R
ATTO Thio12	Tth	C3R, L2R

To attach a linker to your structure, edit your PDB file in your favorite text editor and choose an attachment point.

ATOM       18   CA  ILE E 3              4.144 36.258 39.575 1.00 7.14        C

Change the residue name (ILE) to the linker residue name (ex. C1R) and delete the rest of the residue:

ATOM       18   CA  C1R E 3              4.144 36.258 39.575 1.00 7.14        C

Append the PDB file with the C99 atom of your dye (ex. Alexa Fluor) 488 after the TER card:

ATOM       1317 N   ASN E 163           19.398 31.025 41.679 1.00 38.17       C
TER        1318     ASN E 163
ATOM       1319 C99 A48 E 164

You can then use LEaP to load the AMBER-DYES in the AMBER force field. In this process, you will define atom types, load the topologies for the dye and linker residues, load the updated PDB file, set a bond between the dye (always atom C99) and linker (always atom N99), and relax the structure.

source leaprc.amberdyes 
        pdb = loadpdb 1481.pdb 
        bond pdb.A48.C99 pdb.C1R.N99 
        select pdb.A48 
        select pdb.C1R 
        relax pdb 
        saveAmberParm pdb prmtop inpcrd

For more information on fluorescent dyes, please check out the Amber Reference Manual.