Dear GROMACS users, I started to work with gromacs (version 4.0.5) only several weeks ago and I need your help. Now I am trying to add a new *isopeptide bone* to connect Lys and Gly (to make a dimer of *ubiquitin*). I use AMBER force field.
What I did: 1. Added new type of residues to ffamber.rtp LIQ – LYN that is close enough to GLY (GLQ) to make an isopeptide bond. Distance – 0.13 2. I added this line to specbond.dat: LYN NZ 1 GLY C 1 0.13 LYQ GLQ 3. Added new bond type, angle type and dihedral type to ffamber99bon.itp: For example: [ angletypes ] ; i j k func th0 *cth* HW OW HW 1 104.520 836.800 ; TIP3P water HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds) C C O 1 120.000 669.440 ; new99 ......................................... new lines: C CT N3 1 110.100 527.184 ; FOR UBIQ YULIAN line 344 C N3 H 1 120.000 418.400 ; FOR UBIQ YULIAN N3 C O 1 122.900 669.440 ; FOR UBIQ YULIAN CT C N3 1 116.600 585.760 ; FOR UBIQ YULIAN C N3 CT 1 121.900 418.400 ; FOR UBIQ YULIAN C N3 H 1 120.000 418.400 ; FOR UBIQ YULIAN Here I added a new angle types just by copying a close type of angle in simple peptide bone and changing N to N3 (for isopeptide bone) 4. But in ffamber99.atp one can found that these atoms are different (sp2 and sp3 type of hybridization): amber99_34 14.01000 ; N sp2 nitrogen in amide groups amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) 5. I checked in PyMol the real value of different angles in isopeptide bond and found, of course, that they are differ from angles in simple peptide bond. 6. So when I change N to N3 I did not get a real isippeptide bone. And my *question *is: How to make a new isopeptide bone with correct value of angles and dihedrals. I can simply change the value of angle (by measuring in pymol), but I do not know what is *cth * in [ angletypes ] section of ffamber99bon.itp and how to change it correctly. P. S. After this change I have such a warning in gromacs runnings "WARNING 1 [file ffamber99bon.itp, line 344]: Overriding Angle parameters. old: 111.2 669.44 111.2 669.44 new: C CT N3 1 110.100 527.184" What does it really mean (during editing ffamber99bon.itp I just added several lines and did not remove anything)? Sincerely, Yulian Gavrilov
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