Hi, if you are creating the .itp of a molecule in OPLS, i recomend you to first to optimized the geometry using Quantum Calculations, and also you the appropiate Basis set, and also calculate the atom charges. You could use this software http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-50532008000700031, but you have to be carefull, because the software is selecting atoms from the OPLS.itp, and you have to look if this selection is appropiated. Also, if you are going to use this .itp, try first different MD simulations, and check different properties in order to know if this .itp is doing a good job.  I hope this help you

Hi Andrés,

I tried creating topology using MKTOP and gave the following command:

mktop.pl -i ZnO.pdb -o ZnO.top -ff opls

but there was error msg despite of running chmod: mktop.pl: command not found.

I also made changes in the OPLSAA forcefield files thereby adding parameters for Zn atom.

Hi, well i don't exactly the error msg, perhaps you should check if the .pdf file has the connect info, and also you have to change the $gromacs_dir in the file. with you OPLS folder, remember that you need the charges; The one i am sending you is mk_top_2.2.1.pl. You have to call that file mktop_2.2.1.pl ...., and chmod u+rxw  mktop_2.2.1.pl . to give it permissions 

You said you have added the parameters for the Zn atom; you should also check if you have the other bonding interaction , such as Zn=O and other angles, and dihedrals that might be present in your structure.

And i found this paper, i dont know if this could help you

http://pubs.rsc.org/en/Content/ArticleLanding/2013/CP/c3cp52198b#!divAbstract

I hope this help you,

Dear Andrés,

Since I am new to command lines, I am unable to run the script. I am not able to change the $gromacs_dir in the file. In the script I changed the following: $gromacs_dir="/home/deepali/Desktop/np but it does'nt seem to be right.

The perl script is in np folder. I ran chmod also but getting the same error as I mentioned above. I think it is not able to find the command in the working directory.

Thanks

Dear Deepali, i think you should check this

First, $gromacs_dir must be the path where is the 'top' folder of your grimaces installation, because in this 'top' folder is the 'ops.ff' folder (check the right path)

Second, you must open your terminal and enter to the folder where is located (Open Terminal and change the directory to the one containing the script) the mktop script, and you should use chmod in order to give the scripts permissions (so use 'ls' to check if your script file is there).

I Hope this helps you, Andrés

Hi,

Actually I copied oplsaa forcefield in my working directory and made changes in the files (.rtp, .atp, .dat, .n2t and .itp files) for parameters of ZnO. If $gromacs_dir path is followed then I doubt the topology would be built because there oplsaa forcefield does'nt have parameters for ZnO.

Ok, That's right, i thought you modified the ops.ff in your original folder, in that case change the gromacs_dir, to the folder there the ops.ff is located

Hi,

I could run the following command: perl mktop_2.2.1.pl -i ZnO.pdb -o topology.top -ff opls

but it says:

You have to set the -conect option. Aborting.

could u plz tell me how to add -conect.

thanks for helping me out with ur suggestions.

cheers,

deepali

Hi,

well that info should be in your .pdb file, i heart about this software http://www.exorga.com/EXORGA4.HTM or pymolbut or http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/pdbplugin.html (a VMD pdbplugin), or doing by your own.The connect info is the info of how are bonding your atoms (so check they are OK). You are also going to need the atoms charges, those must be calculated using QM calculations, after geometry optimization.

Andrés

Hi,

CONECT record is present in my pdb file already. I tried adding -conect in the commandline:

perl mktop_2.2.1.pl -i ZnO.pdb -conect -o topology.top -ff opls

prompt is:

Unknown value. Use yes or no. Aborting. when I enter yes, y runs.......

Cheers

Deepali

have you tried, perl mktop_2.2.1.pl -i ZnO.pdb -conect yes -o topology.top -ff opls ?

Try to go to the source code to have a better understanding about what the line at which you had the error is used for. Maybe, this way can be the fastest way to fix the problem.