Yes, I checked topol.top. There are all isopeptide bonds ,that I want (according to atom contacts, angles, etc.)
2011/3/13 Mark Abraham <[email protected]> > On 13/03/2011 9:53 PM, Yulian Gavrilov wrote: > > Thank you! > > I use the correct “O” in Gly according to .rtp and I checked it with vmd. > There is really a new isopeptide bond. When there is no bond, after > minimization and equilibration, Gly and Lys just close to each other but > they are not connected (in vmd). In my case they are connected (in vmd, > pymol). > > > None of these visualization programs read the topology in your .top file. > They just make guesses based on the geometry of the atoms in the coordinate > file. Anything you see that it guessed is irrelevant. Read your pdb2gmx > output, and go and look at the topology to see what atoms have made a bond. > > Mark > > > When I look on step...pdb, one these residues is exploded (it's atoms are > far from each other outside of the water box). > > > 2011/3/13 Mark Abraham <[email protected]> > >> On 13/03/2011 8:55 PM, Yulian Gavrilov wrote: >> >> 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. >> >> >> IIRC, this creates a bond between the lysine side-chain amine N and >> glycine *backbone* carbonyl C. You must use the atom name for the side-chain >> carbonyl carbon (see .rtp entry for GLY). If you've done this wrong, then >> specbond will probably not have made a bond, because the backbone carbonyl C >> was too far away. You should check your pdb2gmx output carefully. >> >> >> >> 1. >> 2. >> >> 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. >> >> >> Seems like a reasonable hypothesis - but do look at 2454 and 2456 as >> well. You have to get out your trajectory and a visualization package and >> see what is actually going wrong. The warnings can be symptomatic of a >> problem that started elsewhere. >> >> You say you've added new interaction types, but I see no reason why you >> would need to. It's chemically so similar to a backbone peptide that you may >> as well keep things the same and model it the same way. Regardless, you >> should probably check that the specbond.dat mechanism has created >> interactions that make sense. Compare with a normal peptide bond. >> >> Mark >> >> >> Please can you advice me how yo make this isopeptide bond good? >> >> Can I just remove this hydrogens? >> >> -- >> >> Sincerely, >> >> Yulian Gavrilov >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > Sincerely, > > Yulian Gavrilov > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sincerely, Yulian Gavrilov
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
