Thank you so much for your quick answer! Now I can access the file and I was wondering how to get amber data for specific molecules. I know that the GLYCAM parameters exist, but as far as I understand I can see only bond information. If, for alanine, the amber.dat file has the following:
ALA N -0.415700 1.8240 N ALA H 0.271900 0.6000 H ALA CA 0.033700 1.9080 CT ALA HA 0.082300 1.3870 H1 ALA CB -0.182500 1.9080 CT ALA HB1 0.060300 1.4870 HC ALA HB2 0.060300 1.4870 HC ALA HB3 0.060300 1.4870 HC ALA C 0.597300 1.9080 C ALA O -0.567900 1.6612 O I was wondering how I could get this info for SIA (Sialic Acid). Is there any library where I could get it in this format? Or maybe some tool to get them from pdb information (if feasible, I am brainstorming!) Thanks again for your help and for your help in advance, Mario -----Original Message----- From: Thomas Holder <thomas.hol...@schrodinger.com> Sent: Monday, June 15, 2020 9:37 AM To: Mario Garcia Urena <ma...@cmcassist.dk> Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] APBS plugin for Sugars Hi Mario, Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, the AMBER force field data files can be found like this: $ find . -name "AMBER.*" ./lib/python3.7/site-packages/src/dat/AMBER.names ./lib/python3.7/site-packages/src/dat/AMBER.DAT Hope that helps. Cheers, Thomas > On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena <ma...@cmcassist.dk> wrote: > > Hi all, > > I was trying to generate dipole moments with pymol using the APBS plugin. For > proteins I adapted a code and the dipole moments are correct and work just > fine, but for sugars it does not. I am well aware that the problem is that > many of the residues are not present in the AMBER force field data (or the > force field I want to use.) In APBS it is relatively easy to adapt and > introduce the sugars’ information manually, however in the APBS plugin for > pymol gets a little bit thorny. I cannot seem to find the files where I > should store the sugar information. Has anybody done this before? Any > alternatives with other programs or approaches are also welcome. > > Thank you in advance, > > Mario > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
