Load the ions library (amber11/dat/leap/lib/ions.lib).

Note: The total charge of the simulated system should be zero, which can be achieved by adding three sodium or potassium ions.

Hi Subhanjan,

Did you build your force field parameters with antechamber? Iodide ion supported by Amber.

I want to use ff99SB force field.I cant find iodide ion in ff99SB. I find iodide ion in ff10 force field.I tried to add iodide ion in the system.but the following message appears when the .prmtop and .inpcrd are attempted to be generated.

>saveamberparm x acd.prmtop acd.inpcrd

Checking Unit.

WARNING: The unperturbed charge of the unit: -3.001000 is not zero.

 -- ignoring the warning.

Building topology.

Building atom parameters.

For atom: .R.A Could not find type: I-

For atom: .R.A Could not find type: I-

For atom: .R.A Could not find type: I-

Parameter file was not saved.

Martiniano Bello Martin Klvana

I tried to build force field parameters of iodide ion in with antechamber.but it give the error message

> "too few atom"

Martiniano Bello

Subhanjan Majumder , post the entire set of commands that you have used in the attempt to generate the topology file.

Hi Subhanjan,

Could you attach the file used to create your file in antechamber?

Following command I used to create the .mol2 file from which I want to create the .frcmod file.I prepare iodide ion in gaussview.pdb file is attached here with. Martiniano Bello Martin Klvana

./antechamber -i iodide.pdb -fi pdb -o iodide.mol2 -fo mol2 -c bcc -s 2 -nc -1

Hi Subhanjan,

You dont have to create the iodine force field since it is supported by amber force field. Initially, I have understood that you tried to create the force field of your ciclodextrin including iodine atom but I understand now that you try to add iodine ions in your simulation box with ciclodextrin in it. So, you have to construct your system with leap and in the step of adding ions follow the next instruction:

addions complex IOD (number of ions according to system charge)

Hi Martiniano,

I tried both.First I tried to create .prmtop and .inpcrd file of a system containing cyclodextrin and iodide.But I failed.Then I tried to add iodine ion in cyclodextrin system.I used ff99SB force field.but I think ff99SB does not contain iodide ion.then I tried ff10 which is a older version.Then it give the following error message.

>saveamberparm x acd.prmtop acd.inpcrd

Checking Unit.

WARNING: The unperturbed charge of the unit: -3.001000 is not zero.

 -- ignoring the warning.

Building topology.

Building atom parameters.

For atom: .R.A Could not find type: I-

For atom: .R.A Could not find type: I-

For atom: .R.A Could not find type: I-

Parameter file was not saved.

Martiniano Bello

Subhanjan Majumder , if the iodide ions are included in the structural file, load the ions library (see my first comment); if the iodide ions are not included in the structural file, add them using the addions command as suggested by Martiniano Bello .