PRODRG2 - will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.

more information in:

http://davapc1.bioch.dundee.ac.uk/prodrg/

This depends on which force field you want to use. If you want to use GROMOS force field, you may try ATB (http://compbio.biosci.uq.edu.au/atb/index.py) server for initial force field paramters of the molecule.

PRODRG2 - will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.

more information in:

http://davapc1.bioch.dundee.ac.uk/prodrg/

But if you use these parameterization servers, please check the outcomes carefully! Sometimes, they don't get the charges or even atom types correctly. See the Gromacs homepage for information about the "parameterization of novel molecules" and have a look at this very nice publication. http://pubs.acs.org/doi/abs/10.1021/ci100335w

Copy and paste the coordinates from pdb file of the molecule to the PRODRG server. It will generate the gro and itp files. Then you can include that itp file into the .top file.

Best Regards,

Hi, I am hoping you are still on this problem.

ATB and PRODRG servers are good options to generate itp and gro files of the molecule as suggested above. If you are planning to use Charmm ff then u can try Swissparam server. Be carefull with PRODRG generated files. It usually gives wrong energies so always keep a check on these and correct accordingly.

Regards,

Nutan

It depends on the ff you want use. PRODRG for gromos and antechamber/acpype tools for amber

hi, follow this link to make your .itp file

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html. hope it will help you .

I want to run the Docked-complex simulation using OPLS forcefield for which I have used mktop to generate topology file of ligand for OPLS forcefield. Now, I have the ligand topology.top file but how to use this for simulation process ? How should I include the ligand information to the opls processed .gro file of protein ? Can I get the ligand.gro file for opls forcefieldby any mean?

for example you have created aldn.itp file regarding the available parameters from literature. the prepared itp file should be converted to gro

what do you recommend to convert the itp to gro?

even after that runing pdb2gmx gives error  aldn residue type is not exists in opls database 

Taking a look at aminoacis.rtp file you will see :

[ ALA ]

[ atoms ]

N opls_238 -0.500 1

H opls_241 0.300 1

CA opls_224B 0.140 1

HA opls_140 0.060 1

CB opls_135 -0.180 2

HB1 opls_140 0.060 2

HB2 opls_140 0.060 2

HB3 opls_140 0.060 2

C opls_235 0.500 3

O opls_236 -0.500 3

[ bonds ]

N H

N CA

CA HA

CA CB

CA C

CB HB1

CB HB2

CB HB3

C O

-C N

[ impropers ]

-C CA N H improper_Z_N_X_Y

CA +N C O improper_O_C_X_Y

++++++++++++

how to introduce your molecule improperes, becuse they are usually given by numbers but here _Z_N ?

the link bellow is therefore helpful

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

regards

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

hi gromacs experts

i generate topolgy from PRODRG for ethylene carbonate. but this topology file didnt work for md simulations. it shows error like '[molecule type]' in the .top file. please anyone help me in this regard. thank you

http://charmm-gui.org/?doc=input/ligandrm

You could use this website to generate *.itp files for your small molecules. Hope this helps!