On 7/16/14, 1:42 AM, Sarath Kumar Baskaran wrote:
Dear all, I was using PRODRG for my protein ligand Simulations, Later, I came across the issues of PRODRG topologies on atom charges, and i have been tryiing to correct these problems. I couldnt use ATB since it gives topopology only for GROMOS96 53a5 and 53a6 force field whereas i need for GROMOS96 43a1. There is a program - ITP Adjuster, an utiltity to correct these charges. Journal of Chemistry - Volume 2013 (2013), Article ID 803151, 6 pages ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server. http://dx.doi.org/10.1155/2013/803151 **Is it wise to use this program to correct the PRODRG output ?
Looking briefly through that paper, it seems that the charges are somewhat over-fitted, and in some cases very different from the existing functional groups in the force field. The "validation" they provide simply states that their program changed the charges; it doesn't demonstrate that the topologies are sane.
QM calculations are the first, but not final, step in deriving Gromos-compatible topologies. You can piece together most molecules from existing functional groups; transferability is at the heart of any force field, particularly one built in pieces as the Gromos parameter sets have been.
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