Minimize Structure While keeping charges
Hello, I was wondering if there was a way to read in charges from a .mol2 file in order to use those charges in the minimize structure utility. By default, it seems that minimize structure adds charges which can be a rather time-consuming step. If I already have the charges in a .mol2 file, can these charges simply be used for the minimization? Thanks, Mike
Hi Mike, Unfortunately it is not possible to use the charges directly from a mol2 or pqr file for minimization. Although reading in a mol2 or pqr file with charges will assign the values as atom attributes, subsequently running miminization will still run Add Charge and assign charges, overwriting those values. It is possible to specify your own charges for nonstandard residues (only) using an attribute definition file or Chimera "setattr" commands, as explained here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified> At least, those were the only ways I was able to figure out. Maybe others have come up with some devious workarounds? Sorry about that, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 16, 2012, at 2:48 PM, Michael Tomasini wrote:
Hello, I was wondering if there was a way to read in charges from a .mol2 file in order to use those charges in the minimize structure utility. By default, it seems that minimize structure adds charges which can be a rather time-consuming step. If I already have the charges in a .mol2 file, can these charges simply be used for the minimization? Thanks, Mike
On May 16, 2012, at 2:48 PM, Michael Tomasini wrote:
Hello, I was wondering if there was a way to read in charges from a .mol2 file in order to use those charges in the minimize structure utility. By default, it seems that minimize structure adds charges which can be a rather time-consuming step. If I already have the charges in a .mol2 file, can these charges simply be used for the minimization?
Hi Mike, Though Chimera should probably offer the option of honoring charges that are already assigned, that wouldn't really save you any time here because minimization also requires atom types and therefore the antechamber program that computes charges and atom types would still have to be called -- and there seems to be no option to have antechamber compute only atom types so it would take the same amount of time. I'm sorry I don't really have a solution for you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Michael Tomasini