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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Fri, Oct 11, 2013 at 10:39 AM, <psu4.uic.edu> wrote: > Hi Jason, > > So we also get the same error message recently by using ff12SB in > MMPBSA.py.MPI AmberTools 12/13. " PB Bomb in pb_aaradi(): No radius > assigned for atom 34 CB 2C" > > We would love to change the F90 code in the vi > $AMBERHOME/AmberTools/src/pbsa/sa_driver.F90. However, since we might not > know the definition of "34 CB 2C" clearly here, we are not 100 % sure which > atom it is and where we should correct/modify in this "sa_driver.F90" > script. > > In the $AMBERHOME/AmberTools/src/pbsa/sa_driver.F90, > > ################################# > ! safe-guarding, very important! > > do iatm = 1, natom > > if ( isymbl(iatm)(1:1) == 'H' ) cycle > > if ( radi(iatm) == ZERO ) then > write(6, *) 'PB Bomb in pb_aaradi(): No radius assigned for atom', > *iatm, igraph(iatm), isymbl(iatm)* > call mexit(6, 1) > endif > > enddo > ################################ > > May I know what *iatm, igraph(iatm), isymbl(iatm) *mean?* > > * > * *When xleap generates this parameter file of which pb_aaradi encounters > the error, the corresponding pdb file is also generated. From this pdb > file, our wild guess is that this atom is the atom number 34 and it is the > beta carbon of the leucine (iatm = atom number), the atom type is amino > acid C beta. (atom type = igraph(iatm) ) * > * > > ATOM 34 CB LEU 3 16.916 -12.796 -0.310 1.00 0.00 > > Here is the prmtop file of which pb_aaradi encounters this error: > > %VERSION VERSION_STAMP = V0001.000 DATE = 09/25/13 20:13:44 > %FLAG TITLE > %FORMAT(20a4) > default_name > %FLAG POINTERS > %FORMAT(10I8) > 4005 17 2002 2042 4552 2768 8994 8937 > 0 0 > 22044 261 2042 2768 8937 104 233 271 > 58 0 > 0 0 0 0 0 0 0 0 > 71 0 > 0 > %FLAG ATOM_NAME > %FORMAT(20a4) > N H1 H2 H3 CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG CD1 HD1 > CE1 > HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA *CB* HB2 HB3 CG HG > CD1 HD11 > > In the prmtop file, it does say this atom is an CB. Not pretty sure why > pb_aaradi still have issues to deal with this particular atom. Does this > error message suggest we should change this "CB" to "C2"? > > We also try the other route by using parmed.py. In parmed.py, > > either > > change AMBER_ATOM_TYPE .%2C C > > or > > change AMBER_ATOM_TYPE .%CB C > > or > > change AMBER_ATOM_TYPE :LEU.CB C > > or > > change AMBER_ATOM_TYPE :LEU.CB 2C > > All will bring the same error message: "CalcError: complex.prmtop!" > > Could you kindly let us know if any solution? > > Cheers, > Henry > > > > > > > > > > On Tue, Aug 7, 2012 at 8:34 AM, Jason Swails <jason.swails.gmail.com> wrote: > >> On Tue, Aug 7, 2012 at 9:03 AM, Vlad Cojocaru < >> vlad.cojocaru.mpi-muenster.mpg.de> wrote: >> >> > Dear Amber users, >> > >> > We are trying to use MMPBSA (AMBER12 + AmberTools 12) to estimate the >> > binding affinity of a protein to DNA. However, when we try to use the >> > non-linear Poisson Bolzmann (npbopt=1) with the the non-polar solvation >> > free energy estimated using the cavity and dispertion terms approach >> > (inp=2), we are getting the error "PB Bomb in pb_aaradi(): No radius >> > assigned for atom 14 CG C6" (see details below). The atom is a CG in a >> > ASP (C6 atom type in the ILDN-modified ff99SB force field). Please see >> > details of the run below. >> > >> >> The problem here is that the ILDN force field appears to not be frequently >> used, at least by those that work on PBSA (it's hard to keep up with all of >> the core atom types used by all of the force fields out there). >> >> There are 2 straightforward solutions to this issue. >> >> You can go through the sa_driver.F90 code (in >> $AMBERHOME/AmberTools/src/pbsa/) and add in recognition for the C6 atom >> type where you think it belongs (I think you may have to do this for >> multiple routines). >> >> Alternatively, you can use xparmed.py to change the atom type names from C6 >> to C, which is the 'official' Amber force-field type for that particular >> atom (this will NOT change any parameters, just the name of the atom type). >> To take this approach, use the "change" command with the AMBER_ATOM_TYPE >> keyword (if you are using the GUI, you can use the arrow buttons to scroll >> to that key). The selection mask should be .%C6 to select all C6 atom >> types (or you can use :ASP.CG -- just make sure you capture all of the >> atoms you want to capture). Then set C as the new value. >> >> Now, if we use inp=2 and radiopt=0 (radii taken from the topology file; >> > we know we should not do this in principle - but we did it for testing), >> > the same error occurs. >> > However, if we use inp=1 and radiopt=0, MMPBSA runs but it gives >> > abnormal results (in the range of +4000 kcal/mol .. obviously a >> non-sense). >> > When we use inp=0 and radiopt=0, we get a better result (in the range of >> > -100 kcal/mol) but here we do not take into account the non-polar >> > solvation free energy >> > MMGBSA runs fine with the same system and gives reasonable values at >> > first glance (in the range of -200 kcal/mol). >> > >> > Could anybody explain this error message? Are we doing something wrong >> > here ? >> > >> > Also an additional question: how should we control the SASA calculation >> > in MMBSA ? ssaopt=0, saopt=0 are defaults. Does this mean that by >> > default no estimation of SASA is done since saopt=0? Does the gbsa >> > parameter play any role for MMPBSA or is used just for GB calculations ? >> > >> >> gbsa does nothing except for GB calculations. >> >> HTH, >> Jason >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Candidate >> 352-392-4032 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > > Pin-Chih Su (Henry Su) > > Ph.D. canditate > > Center for Pharmaceutical Biotechnology (MC 870) > > College of Pharmacy, University of Illinois at Chicago > > 900 South Ashland Avenue, Room 1052 > > Chicago, IL 60607-7173 > > office 312-996-5388 > > fax 312-413-9303 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Oct 11 2013 - 11:00:04 PDT