Thanks! I tried to use ACPYPE previously. That time there's something wrong so it couldn't recognize my pdb file. Now it seems OK. I just got the result. I like it not renaming my atoms, like PRODRG. And its parameter file format is more similar to the file in Xplor-NIH, thus easy to read. My ligand is a heme derived molecule. As a quick check, I picked a pyrrole ring and sum its interior angles equilibrium value. For a planar five-member ring, such value should be equal to 540 degree. ACPYPE gives a result much more than 540 degree, which is geometry impossible. I believe that's because the parameter just comes from GAFF, which is not really optimized for a specific case. While PRODRG just assign each interior angle as 108 degree, although not so precise, at least the ring will be kept planar. So, I really like the writing of ACPYPE. Unfortunately I still cannot use its result directly...
Qinhong Yu The Ames Lab Department of Chemistry University of California, Davis From: Gabriel Cornilescu Date: 2016-07-15 11:22 To: Val Yu CC: xplor-nih Subject: Re: [Xplor-nih] Help on small molecule parameterization Please try and share your impressions: http://webapps.ccpn.ac.uk/acpype/ On Jul 15, 2016, at 2:04 PM, Val Yu <[email protected]> wrote: Hi, Is there any method for small molecule parameterization other than Prodrg? That server doesn't give me satisfy parameters and atom naming of it is terrible. I'm afraid simply modifying this parameter to let result fit my expectation is not accepted. It seems that small molecule parameterization is not an easy task, sometimes itself can be published as a paper (with some simulation result). I'm wondering how you make the ligands work? Any suggestion and experiences will be appreciated because I really know little about this and I don't want to do stupid things. -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
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