Dear AMBERI am trying to test some features in AMBER, one of them is EP.I have added an extrapoint to my ligand and calculated the charge. During leap step I got an the following error:
total atoms in file: 4900 Leap added 1 missing atom according to residue templates: 1 unknown element
This unknown element as I believe is returned to EP atom in my PDB file. But I defined and loaded EP before loading my PDB file. My commands were as following:source leaprc.ff99SBsource leaprc.gaffloadamberparams EP.frcmodMOL = loadpdb MOL.pdb
here is my EP.frcmod
remark goes hereMASSEP 0.0000
NONBONEP 1.0000 0.0000
Am I right? can I use only EP for my ligand with ff99SB force field.If you don't mind, I have used the normal input file as I always do for AMBER MM simulation, depending on AMBER will use the default values for EP treatment (massless off-center charge), is that right? or should I add additional keywords in my input file? (I have read readme file and extrapt file inside sander without any hints).
Thanks in advanceW. Flak
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Received on Sun May 23 2010 - 15:00:03 PDT
