Jordan,

this is a very delicate matter. Which forcefield are you using? For AMBER, there is some detailed description on how to produce new topologies. For GROMOS, it is usually a little more complicated to build such files, and the easier and safer way is to built the new molecule using fragments already existent on the forcefield.

The bonded parameters are easy to obtain. You can use the parameters for the closest residue (if you are in doubt, build the residue, optimize it using some quantum mechanics method and then calculate these parameters). Atomic charges are usually more difficult for GROMOS if there is no equivalent group on the forcefield. Take special care on choosing the proper dihedral parameters. If your residue is too dissimilar from those already in the rtp, you will need to produce a quantum mechanic derived curve for the dihedral and fit it to the molecular mechanics part.

But folding is another delicate subject. You will see the folding in MD simulations for small peptides, but even for something around 20 residues, simulations of hundreds of nanoseconds will be necessary. And, to have a solid characterization of the process, I would recommend to run independent simulations, and also study a solid control with natural residues...

Hugo

Jordan,

this is a very delicate matter. Which forcefield are you using? For AMBER, there is some detailed description on how to produce new topologies. For GROMOS, it is usually a little more complicated to build such files, and the easier and safer way is to built the new molecule using fragments already existent on the forcefield.

The bonded parameters are easy to obtain. You can use the parameters for the closest residue (if you are in doubt, build the residue, optimize it using some quantum mechanics method and then calculate these parameters). Atomic charges are usually more difficult for GROMOS if there is no equivalent group on the forcefield. Take special care on choosing the proper dihedral parameters. If your residue is too dissimilar from those already in the rtp, you will need to produce a quantum mechanic derived curve for the dihedral and fit it to the molecular mechanics part.

But folding is another delicate subject. You will see the folding in MD simulations for small peptides, but even for something around 20 residues, simulations of hundreds of nanoseconds will be necessary. And, to have a solid characterization of the process, I would recommend to run independent simulations, and also study a solid control with natural residues...

Hugo

Hi Jordan,

If you are still working on your force field development, you may find this paper helpful.

http://www.ncbi.nlm.nih.gov/pubmed/15264259

I found it useful when adding a gamma-carboxyglutamic acid to the residue database for my GLA protein. I started by copying the glutamate residue section and renaming it and then adding the atoms, bonds, etc. needed. There are already two glutamates in the aminoacid.rtp, [GLU] and [GLUH] so you will start to see the pattern for adding another. Then I looked up the best parameters in the tables in the article. For instance, if you wanted to use gromos53a6 C-C-C bond with angle theta_0=109.5 and k_theta=520 you use CB CA C ga_13 where ga_13 refers to the information in table 3 of the article bond angle type code 13. The ga_13 will be replaced with the parameters in the ffbonded.itp file when creating the *.tpr file. For new connectivity, study the examples in the last column of the tables and compare the parameters to your QM calculations or similar moieties you find in the force field elsewhere. We found that using the NBO calculation program with GAMESS gave good partial charges for new gromos atoms when H and heavy atom charges are summed together.

http://www.msg.ameslab.gov/gamess/

http://nbo6.chem.wisc.edu/

Also, the general procedure is here:

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

Also, take a look here:

https://atb.uq.edu.au/

Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi

I have read the chapter 5 of manual but i am confuse how can i add residue

into heme atom of .rtp ff

this is the coordinate due to which error come

HETATM 1529  O01 HEM   187       3.996  19.101  70.594  0.00

0.00           O

kindly guide me how i can make changes in the rtp file and .atp so that

this error remove

here is the heme rtp part of my selected ff where i can add O01 and also

tell me these 4 column and these values and tell me which value i add for

O01 like (FE FE 0.40000     0 )

[ HEME ]

  [ atoms ]

    FE    FE     0.40000     0

    NA    NR    -0.10000     0

    NB    NR    -0.10000     0

    NC    NR    -0.10000     0

    ND    NR    -0.10000     0

   CHA     C    -0.10000     1

   HHA    HC     0.10000     1

   C1A     C     0.00000     2

   C2A     C     0.00000     2

   C3A     C     0.00000     2

   C4A     C     0.00000     2

   CMA   CH3     0.00000     3

   CAA   CH2     0.00000     4

   CBA   CH2     0.00000     4

   CGA     C     0.27000     5

   O1A    OM    -0.63500     5

   O2A    OM    -0.63500     5

   CHB     C    -0.10000     6

   HHB    HC     0.10000     6

   C1B     C     0.00000     7

   C2B     C     0.00000     7

   C3B     C     0.00000     7

   C4B     C     0.00000     7

   CMB   CH3     0.00000     8

   CAB   CR1     0.00000     9

   CBB   CH2     0.00000     9

   CHC     C    -0.10000    10

   HHC    HC     0.10000    10

   C1C     C     0.00000    11

   C2C     C     0.00000    11

   C3C     C     0.00000    11

   C4C     C     0.00000    11

   CMC   CH3     0.00000    12

   CAC   CR1     0.00000    13

   CBC   CH2     0.00000    13

   CHD     C    -0.10000    14

   HHD    HC     0.10000    14

   C1D     C     0.00000    15

   C2D     C     0.00000    15

   C3D     C     0.00000    15

   C4D     C     0.00000    15

   CMD   CH3     0.00000    16

   CAD   CH2     0.00000    17

   CBD   CH2     0.00000    17

   CGD     C     0.27000    18

   O1D    OM    -0.63500    18

   O2D    OM    -0.63500    18

thanks