On 6/08/2012 4:31 AM, James Starlight wrote:
Mark,
1) The error was because I've used topology of the CRO generated by
the ATB in the ITP form in the RTP file.
No, the error "Residue 'CRO' not found in residue topology database"
means you haven't put it in the right place, but until you inspect your
pdb2gmx output for clues about where it is looking, to help find where
you haven't followed the right procedure, you're stuck. You've not told
us your command line or shown us any significant output, so you really
can't be helped.
E.g in RTP file I've found that [ atoms ] is simple
C C 0.450 1
when in my ITP its more complicated
7 C 1 CRO C1 5 0.089 12.0110
the main difference is that RTP havent atom order where in IPT file
the order of each group is specified.
Is there any way to convert ITP back to RTP form ?
No. You'll have to do it by hand.
2) I've used specbond.dat to define covalent bonds between C and N
termi of chromophore and corresponded termi of the djacent residues (
in GFP chromophore is covalently linked in the midle of the alph helix
of that protein in both ends)
Sounds like a recipe for trouble, unless you know how to build a
two-chain peptide with correct termini into the same [moleculetype], and
get specbond.dat to work at the same time. It's possible, but why not
use the built in mechanism for head-to-tail peptide linking?
Mark
James
2012/8/5, Mark Abraham <[email protected]>:
James Starlight wrote
Dear Gromac's users!
I'm working with the GFP protein which has chromophore (CRO) group
which is covalently bonded to the protein. I want to add new residue
to the Gromos 53.6 ff. by means of algorithm described here.
For that I've coppied files to my local work dirr and modify all of
them in accordance to the above tutorial- I've coppied .itp of CRO to
the aminoacids.rtp
[ CRO ]
[ atoms ]
etc
I've defined bonds of the djacent real amino acids in the specbond.dat
Seems dangerous from my memory of GFP. You should probably be making a
single residue for the whole chromophore, in which case a model that does
not need specbond.dat is possible.
James Starlight wrote
Finally I've defined CRO (as the protein) in the residuetypes.dat
When I've try use pdb2gmx I've obtain error
Fatal error:
Residue 'CRO' not found in residue topology database
What I've done wrong?
If
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
and its links don't help, you'll have to inspect carefully your output from
pdb2gmx for clues.
Mark
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