Joel Tyndall wrote:
I'm wanting to add in an ATP molecule based on my template to my modelled structure. I have looked at the FAQ and it does seem a laborious task to write the CHARM topology files etc. I was wondering if there was a database of ligands (wiki? type thing) or a web based converter ( i have already looked at Prodrg in dundee) or if someone wants to share their top files for ATP....Or any alternative methods out there? I'm currently using 8v2 but with old scripts and will upgrade soon.
The following link in the Modeller wiki may be of use: http://salilab.org/modeller/wiki/Parameters
If rigid body modeling isn't going to work for you, you may be able to find suitable CHARMM parameters at the CHARMM or NAMD links posted on that page, or a user with existing parameters may help out and post them there.
Ben Webb, Modeller Caretaker
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