Dear gmx users, I just started with gromacs.
Can you help me to find my mistake? I already asked about it, but I did not understand what to do exactly in my case. I try to run to add a new *isopeptide bone* to connect Lys and Gly (to make a tetramer of *ubiquitin*). I use AMBER99 force field, Gromacs 4.0.5. What I did: 1. I changed names of residues according to AMBER rules (LYS to LYN etc.). 2. Added new type of residues to ffamber.rtp (LYN -> LYQ and GLY -> GLQ that are making a new isopeptide bond) and added a new line to specbond.dat (LYN NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a bond. 3. Added new bond type, angle type and dihedral type to ffamber99bon.itp After running of MD (I've got good minimization and equilibration – nvt and npt) I've got such an error: starting mdrun 'Protein in water' 600000 steps, 1200.0 ps. step 94100, will finish Sun Mar 13 08:15:56 2011 Step 94124, time 188.248 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000796, max 0.032792 (between atoms 2454 and 2456) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2454 2457 35.6 0.1522 0.1545 0.1522 And after it the same type of errors with another atoms: 2454 2456 36.1 0.1106 0.1113 0.1090 --> *Gly CA and HA1, HA2* 2454 2455 40.5 0.1114 0.1103 0.1090 ..... 2454 2456 90.0 0.1078 0.1479 0.1090 771 773 48.5 0.1011 0.1012 0.1010 ...... 771 773 39.8 0.1012 0.1005 0.1010 --> *Gly NZ and HZ1, HZ2* 771 772 34.9 0.1012 0.1030 0.1010 ....... 2454 2457 102.1 0.1490 38312886396780544.0000 0.1522 2454 2456 83.0 5.9313 39290317874135040.0000 0.1090 ....... First errors are with atoms from the residues with *new isopeptide bond*. I suppose, that this bond is not good. Please can you advice me how yo make this isopeptide bond good? Can I just remove this hydrogens? -- Sincerely, Yulian Gavrilov
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