On 6/08/2012 6:00 PM, James Starlight wrote:
Mark,
The main difficulties is that ATB's output is in the form like
[ bonds ]
1 2 2 0.1000 1.8700e+07
1 3 2 0.1000 1.8700e+07
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
2 1 4 2 109.50 425.00
3 1 4 2 109.50 425.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
7 8 10 9 2 0.00 167.36
8 10 9 11 2 0.00 167.36
10 9 11 7 2 0.00 167.36
etc
here I must replace the number of atoms by the corresponded real atoms
but also replace the values for the bonds, angles and dihedrals by the
Gromacs type codes ( e.g gb_1 etc). This is very routinely for me yet
:)
You don't need to replace
1 2 2 0.1000 1.8700e+07
with stuff like
Cone Ctwo gb_234
Stuff like
Cone Ctwo 2 0.1000 1.8700e+07
is fine. gb_234 means "paste in the #define in the .itp file"...
(seehttp://www.gromacs.org/Documentation/Include_File_Mechanism) so no need to take it
out to just paste it in again. See discussion in manual 5.6.1, which of course you've
read ;-)
Most of what you need to do is to map the atom numbers back to atom names. Most
of the rest is doing the +N, -C stuff to use the standard peptide linking
machinery.
Mark
I've sent the letter to the ATB's developments with the same
proposition to five RTP as the output which could be in some cases
more usefull that ITP.
James
2012/8/5, Mark Abraham <mark.abra...@anu.edu.au>:
On 6/08/2012 4:11 PM, James Starlight wrote:
Mark,
I suppose that the most trivial way to include such external
topologies is the placement of the ITP file at the bottom of the
topol.top file ( and addition of two covalent bonds with the adjcent
residues in case of GFP chromophore ) like in any potein-ligan system.
No, because bonded interactions can only occur within a [moleculetype].
I think that it must be some script foe convertion itp ro rtp because
both of that formats have a lot of differenties so the manually
editing in case of big HET group is very routinely.
For the ~25 atoms of the GFP chromophore, given a reliable .itp of
Ace-Gly-Cro-Gly-Nme or something, producing an .rtp entry by hand is a
job of up to half an hour, if you understand the .rtp format.
Particularly if the bonded interactions are from the main forcefield,
you've only got to describe atom types, connectivity and charge.
You could make a feature request of the ATB people for .rtp output
(which might come with supplemental forcefield .itp files).
Mark
James
2012/8/5, Mark Abraham <mark.abra...@anu.edu.au>:
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 <mark.abra...@anu.edu.au>:
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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