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--- > N NA N2 N* NC NB NT NY > C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ I am not sure how to include this info in a frcmod file. In any case, I received an email from someone saying that he could not load the HEM parameter files. I wonder why this part of the parm99.dat file was changed. Best, On Wed, 28 Mar 2007, Ilyas Yildirim wrote: > Dear All, > > In AMBER 8, I do not have the problem that I will be describing shortly. I > have a .prepi file and frcmod file for HEME structure (I cannot recall > from where I got it). When I load these files into leap and when I try to > create the prmtop/inpcrd files, I am getting the following error message > (I have attached the files that I am using): > > ------------------------------------------------------------- > # xleap -f xleap1.in > . > . > . > . > . > Building topology. > Building atom parameters. > For atom: .R<HEM 1>.A<NA 2> Could not find type: NP > For atom: .R<HEM 1>.A<CBB 45> Could not find type: CX > For atom: .R<HEM 1>.A<NB 48> Could not find type: NO > For atom: .R<HEM 1>.A<CBC 55> Could not find type: CX > For atom: .R<HEM 1>.A<NC 58> Could not find type: NP > For atom: .R<HEM 1>.A<ND 72> Could not find type: NO > Parameter file was not saved. > ------------------------------------------------------------- > > When I modify the frcmod file and add 3 more lines to the end of frcmod > file (which is the NONBON part), everything works fine: > > ------------------------------------------------------------- > # xleap -f xleap2.in > . > . > . > . > . > <HEM 1>: C3D C4D C2D CAD > <HEM 1>: C4A NA C3A CHB > <HEM 1>: C4B NB C3B CHC > <HEM 1>: C4C NC C3C CHD > <HEM 1>: C4D ND C3D CHA > total 22 improper torsions applied > 20 improper torsions in old prep form > Building H-Bond parameters. > Not Marking per-residue atom chain types. > Marking per-residue atom chain types. > (no restraints) > ------------------------------------------------------------- > > Those 3 lines are just 3 NONBON terms (zero): > > NONBON > FE 1.20000 0.05000 0.00000 > LO 1.60000 0.20000 0.00000 > LC 1.85 0.12 0.0 > NP 0.00000 0.0000 0.00000 > NO 0.00000 0.0000 0.00000 > CX 0.00000 0.0000 0.00000 > > In AMBER 8, I do not have this problem. Moreover, It gives error for the > atom types NP,NO,CX; not for the other ones (There are total 8 new atom > types defined in the frcmod file). > > Does this sound like a bug, or am I missing something here? Thanks in > advance. > > Best, > > -- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - - - University of Rochester - - - Hutchison Hall, # B10 - - - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) - - http://www.pas.rochester.edu/~yildirim/ - ---------------------------------------------------------------Received on Sun Apr 01 2007 - 06:07:19 PDT