MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI MIN: Cycle ENERgy Delta-E GRMS Step-size STEEPD> An energy minimization has been requested.ĮPHI: WARNING. General atom nonbond list generation found:ġ6174130 ATOM PAIRS WERE FOUND FOR ATOM LISTĨ70014 GROUP PAIRS REQUIRED ATOM SEARCHES = PRIMARY = SPACE FOR 19429274 ATOM PAIRS AND 0 GROUP PAIRS VEHEAP> Expanding heap size by20054016 words. = PRIMARY = SPACE FOR 12952836 ATOM PAIRS AND 0 GROUP PAIRS VEHEAP> Expanding heap size by13565952 words. WARNING: ATOMS RNA9 747 CYT H42 AND RN10 425 GUA H21 ONLY 1.45 A. WARNING: ATOMS RNA6 533 GUA H22 AND RNA6 544 CYT H42 ONLY 1.39 A. WARNING: ATOMS RNA4 697 GUA H1 AND RN13 807 ADE H2 ONLY 1.26 A. WARNING: ATOMS RNA4 689 ADE H8 AND RNA9 752 GUA H22 ONLY 1.05 A. = PRIMARY = SPACE FOR 8635211 ATOM PAIRS AND 0 GROUP PAIRS Generating nonbond list with Exclusion mode = 5 with mode 5 found 58548 exclusions and 27088 interactions(1-4) There are 0 group pairs and 0 group exclusions. There are 0 atom pairs and 0 atom exclusions. SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500ĬHARMM> minimize sd nstep 50 cdie eps 1.0 fshift vshift cutnb 13.0 ctofnb 12.0ĮLEC VDW ATOMs CDIElec FSHIft VATOm VSHIftĬUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 Number of selected atoms: 1591ĬHARMM> ! First used Steepest Descent (a gentle minimizer) SELRPN> 1591 atoms have been selected out of 37533ĪBSOlute type as set number 3. Number of selected atoms: 2806ĬHARMM> cons harm force 20.0 sele. SELRPN> 2806 atoms have been selected out of 37533ĪBSOlute type as set number 2. The force constant of 20.00000 will be used. Mass weighting will NOT be used for new restraints. Reference coordinates set to main coordinates. SELRPN> 2526 atoms have been selected out of 37533ĪBSOlute type as set number 1. what are the consequences of this error for the minimization?Īnd also - what are the consequences if such error- are some of the bond lengths fixed?ĬHARMM> ! Harmonic constraints on all protein atomsĬHARMM> cons harm force 20.0 sele. type O3') endĬons harm force 5.0 sele segid L4. type O3') endĬons harm force 5.0 sele segid RN10. type O3') endĬons harm force 5.0 sele segid RNA7. type O3') endĬons harm force 5.0 sele segid RNA4. ! then small constraints on backbone onlyĬons harm force 5.0 sele segid RNA1. segid L4 endĬons harm force 0.0 sele segid RNA7. Write psf card name all_min_testMMPBSA.psfĬons harm force 0.0 sele segid RNA1. Write coor card name all_min_testMMPBSA.crd segid L4 endĬons harm force 10.0 sele segid RNA7. ! Reduce harmonic constraints and minimize some moreĬons harm force 10.0 sele segid RNA1. segid L4 endĬoor orie rms sele segid RNA7.
Minimize sd nstep 50 cdie eps 1.0 fshift vshift cutnb 13.0 ctofnb 12.0Ĭoor orie rms sele segid RNA1. ! First used Steepest Descent (a gentle minimizer) segid L4 endĬons harm force 20.0 sele segid RNA7. ! Harmonic constraints on all protein atomsĬons harm force 20.0 sele segid RNA1. ! Save coordinates also in comparsion coordinate set for later use Read param card name par_all27_prot_na.inp
! Get definitions of amino acids and standard parameters ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE ".** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE I'm using the standard "bonh param" and what i get is
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