I need to create a topology file (.top for GROMACS) of 2,3,7,8-TCDD (dioxin).
In particular my topology file will have to be suited for implementing OPLS-AA forcefield, since I know that the latest releases of this ff considers halogen bonding interaction.
I found the PRODRG server to accomplish such task, but unfortunately this service offers topologies for GROMOS 43a1 ff.
Do you know any similar tool for OPLS-AA? Or, better, do you know in literature topolgies for TCDD?
I have no idea if anyone has used my program, and there is nothing to cite; it's not a published algorithm. TopolGen is just a short script I wrote and contributed to the Gromacs software repository because others might find it useful. It makes no attempt to derive suitable charges; it guesses both charges, connectivity, and atom types from the input coordinates. It is meant to be a starting point topology that can be refined. For simple molecules, it works very well. For complex molecules, you will likely have to re-calculate charges, but that is rather easy to do.
I wrote a script that writes an OPLS-AA topology from an input PDB file, called TopolGen. You can download it (version 1.1) from http://www.gromacs.org/Downloads/User_contributions/Other_software.
The caveat is that it attempts to guess connectivity simply from the order of the atoms, so it's not always smart and it's not always right. Atom types and charges usually need some refinement, but luckily the OPLS-AA procedures for tuning parameters are very well documented.
MKTOP is also a popular program:
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-50532008000700031&lng=en&nrm=iso&tlng=en
http://www.aribeiro.net.br/mktop/
I have found mktop elsewhere. For what concern TopolGen is there any related paper for citing it?
I have no idea if anyone has used my program, and there is nothing to cite; it's not a published algorithm. TopolGen is just a short script I wrote and contributed to the Gromacs software repository because others might find it useful. It makes no attempt to derive suitable charges; it guesses both charges, connectivity, and atom types from the input coordinates. It is meant to be a starting point topology that can be refined. For simple molecules, it works very well. For complex molecules, you will likely have to re-calculate charges, but that is rather easy to do.
Try the Antechamber (tools from the AMBER site) and acpypi (google it). This will construct a set of useful topolgies etc...
Antechamber is free. It is part of AmberTools, which is separate from the main Amber software. ACPYPE is also free.
Try the ACPYPE together the MKTOP. I created a Linux distribution based on Ubuntu 12.10 (ARLINUX) with the acpype, mktop and various others program installed to molecular modeling calculation. The download link is: https://dl.dropboxusercontent.com/u/95651470/arlinux-dist.iso
If not off-topic, what about a topology generator for OPLS-AAM in charmm format? And general guidelines on how to deal with OPLS-AAM for non proteins. At first glance, OPLS-AAM appears to be a proprietary world, far from the guidelines available for charmm ff, quite bad for namd users, like me
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