Hi, I have an itp. I will send it to you off list.
Cheers Tom On 04/11/2014 06:43 PM, Stephen N. Floor wrote:
Hi gromacs users - I am trying to simulate a protein-ATP complex and am trying to add parameters for ATP to the forcefield amber99sb-ildn. First off, I find it likely that someone has already done this - is there an .itp file for ATP floating around somewhere with the recommended parameters from Meagher, Redman & Carlson, JCC (2003)? http://www.ncbi.nlm.nih.gov/pubmed/12759902 If not, I am trying to decide between using parms generated from PRODRG (which spits out a .itp, albeit with non-amber atom types) versus editing the ffbonded and ffnonbonded files for the forcefield to include bond, angle, and dihedral parms from Meagher 2003. Any thoughts on this? I am partial to using parameters from Meagher 2003 since they did a full QM treatment of the ligand and these are recommended by Bryce. I tried to follow previous messages in the gmx-users list on this topic, but am stuck translating dihedrals from the AMBER94 FRCMOD file to ffbonded.itp, as recommended in a previous thread (http://gromacs.5086.x6.nabble.com/Re-AMBER-force-fields-for-ATP-td4440113.html) For the AMBER94 PREP and FRCMOD files please see here: http://www.pharmacy.manchester.ac.uk/bryce/amber/ I think I could generate input files that would be properly parsed, but am looking for verification that I'm doing it correctly before conducting simulations with incorrect parameters. Thanks for your time. -Stephen -- Stephen N. Floor HHMI Fellow of the Helen Hay Whitney Foundation Doudna Group http://doudna.berkeley.edu
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