AMBER Archive (2005)

Subject: AMBER: FATAL error with ATP, MG2 residue

From: Michael Mazanetz (paxmm2_at_nottingham.ac.uk)
Date: Thu Nov 17 2005 - 03:41:12 CST

Dear AMBER forum, I am running AMBER on an SGI, IRIX. Previously I've not have difficulties creating standard protein top and crd files. But when I try to generate prmtop and inpcrd files for a non-standard ATP molecule I get error messages. I've searched the web for answers but couldn't find anything that improved the result. Here is what I do: I've created a new pdb file which includes the two waters, Mg and ATP./users/mazzo/PDB_FILES/ B01_058_110_003.pdb If simply loaded this pdb file above into XLeap at this point the vast majority of the file would load OK. There would be problems, however, with the non-standard ATP residue. Before I can successfully load the B01_058_110_003.pdb file into XLeap I need to tell it what the non-standard unit is.I need to create a library file for our ATP unit. The quickest way to do this, since we need an initial structure for this unit, is to simply cut out ATP of the B01_058_110_003.pdb file and save it as its own pdb file. There is already a parameterized ATP available in the literature:1 So I load up XLEaP and run the following commands: $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03 > loadAmberPrep ATP.prep> loadamberparams frcmod.phos> ATP = loadpdb ATP.pdb> edit ATP> desc ATP> saveoff ATP atp.lib> loadoff atp.lib> cdknew3 = loadpdb B01_058_110_003.pdb> list> saveamberparm cdknew3 B01_058_125_001.prmtop B01_058_125_001.inpcrd Then it dies.... here are the complete details: > loadAmberPrep ATP.prepLoading Prep file: ./ATP.prep > loadamberparams frcmod.phosLoading parameters: ./frcmod.phosReading force field mod type file (frcmod)> ATP = loadpdb ATP.pdbLoading PDB file: ./ATP.pdb total atoms in file: 31 > edit ATP> desc ATPUNIT name: Head atom: nullTail atom: nullContents: R<ATP 1> > saveoff ATP atp.lib Creating atp.libBuilding topology.Building atom parameters.> loadoff atp.lib> cdknew3 = loadpdb B01_058_110_003.pdbLoading PDB file: ./B01_058_110_003.pdb (starting new molecule for chain D) (starting new molecule for chain )Created a new atom named: MG2 within residue: .R<MG2 441> Added missing heavy atom: .R<MG2 441>.A<MG 1> total atoms in file: 3572 Leap added 3553 missing atoms according to residue templates: 1 Heavy 3552 H / lone pairs The file contained 1 atoms not in residue templates > listACE ALA ARG ASH ASN ASP ATP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL WAT cdknew3 frcmod03 parm99 > saveamberparm cdknew3 B01_058_125_001.prmtop B01_058_125_001.inpcrdChecking Unit.WARNING: There is a bond of 3.277331 angstroms between: ------- .R<NSER 293>.A<CB 7> and .R<NSER 293>.A<OG 10>WARNING: The unperturbed charge of the unit: 1.000000 is not zero.FATAL: Atom .R<ATP 440>.A<PG 1> does not have a type.FATAL: Atom .R<ATP 440>.A<O1G 2> does not have a type.FATAL: Atom .R<ATP 440>.A<O2G 3> does not have a type.FATAL: Atom .R<ATP 440>.A<O3G 4> does not have a type.FATAL: Atom .R<ATP 440>.A<PB 5> does not have a type.FATAL: Atom .R<ATP 440>.A<O1B 6> does not have a type.FATAL: Atom .R<ATP 440>.A<O2B 7> does not have a type.FATAL: Atom .R<ATP 440>.A<O3B 8> does not have a type.FATAL: Atom .R<ATP 440>.A<PA 9> does not have a type.FATAL: Atom .R<ATP 440>.A<O1A 10> does not have a type.FATAL: Atom .R<ATP 440>.A<O2A 11> does not have a type.FATAL: Atom .R<ATP 440>.A<O3A 12> does not have a type.FATAL: Atom .R<ATP 440>.A<O5* 13> does not have a type.FATAL: Atom .R<ATP 440>.A<C5* 14> does not have a type.FATAL: Atom .R<ATP 440>.A<C4* 15> does not have a type.FATAL: Atom .R<ATP 440>.A<O4* 16> does not have a type.FATAL: Atom .R<ATP 440>.A<C3* 17> does not have a type.FATAL: Atom .R<ATP 440>.A<O3* 18> does not have a type.FATAL: Atom .R<ATP 440>.A<C2* 19> does not have a type.FATAL: Atom .R<ATP 440>.A<O2* 20> does not have a type.FATAL: Atom .R<ATP 440>.A<C1* 21> does not have a type.FATAL: Atom .R<ATP 440>.A<N9 22> does not have a type.FATAL: Atom .R<ATP 440>.A<C8 23> does not have a type.FATAL: Atom .R<ATP 440>.A<N7 24> does not have a type.FATAL: Atom .R<ATP 440>.A<C5 25> does not have a type.FATAL: Atom .R<ATP 440>.A<C6 26> does not have a type.FATAL: Atom .R<ATP 440>.A<N6 27> does not have a type.FATAL: Atom .R<ATP 440>.A<N1 28> does not have a type.FATAL: Atom .R<ATP 440>.A<C2 29> does not have a type.FATAL: Atom .R<ATP 440>.A<N3 30> does not have a type.FATAL: Atom .R<ATP 440>.A<C4 31> does not have a type.FATAL: Atom .R<MG2 441>.A<MG2 2> does not have a type.Failed to generate parametersParameter file was not saved. References: (1) Meagher, K. L.; Redman, L. T.; Carlson, H. A. J Comput Chem 2003, 24, 1016-25. If anyone has any suggests please send me an email.Thanks,Mike Mazanetz

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