James Starlight wrote:
Justin, hello!
I've found that D and L-isomers must be topological identicaly so I've
used topology of Leu and Val residues for Dle and Dva resp.
I've added information about topology of that two residues to the .rtp
.hdb of my force field as well as to the
<http://www.gromacs.org/Documentation/File_Formats/.rtp_File>residuetypes.dat
<http://www.gromacs.org/Documentation/File_Formats/residuetypes.dat>
Then I've succsesfull generated topology for gramicidin via pdb2gmx.
I have only questions about two terminal CAP groups used in the Gramicidin
It was FOR group on the C-end
HETATM 1 C FOR A 1A -3.690 -1.575 -2.801 1.00
0.00 C
HETATM 2 O FOR A 1A -3.774 -1.363 -1.586 1.00
0.00 O
HETATM 3 H FOR A 1A -4.305 -1.047 -3.545 1.00
0.00 H
and the ETA group on the N-end
HETATM 267 C1 ETA A 15A 5.148 -0.421 8.762 1.00
0.00 C
HETATM 268 C2 ETA A 15A 3.657 -0.080 8.832 1.00
0.00 C
HETATM 269 N ETA A 15A 2.813 -1.244 8.933 1.00
0.00 N
HETATM 270 O ETA A 15A 5.921 0.752 8.985 1.00
0.00 O
HETATM 271 1HN ETA A 15A 2.507 -1.491 9.845 1.00
0.00 H
HETATM 272 HO ETA A 15A 5.736 1.339 8.244 1.00
0.00 H
HETATM 273 1H1 ETA A 15A 5.410 -1.174 9.531 1.00
0.00 H
HETATM 274 2H1 ETA A 15A 5.374 -0.849 7.759 1.00
0.00 H
HETATM 275 1H2 ETA A 15A 3.383 0.525 7.938 1.00
0.00 H
HETATM 276 2H2 ETA A 15A 3.492 0.565 9.718 1.00 0.00
I could not find good analogue for that groups in Amber force field so
I've desided to deleate that groups temporary.
Could you tell me how I can add possible Caps on the C and N terms of
each chain of my molecule via pdb2gmx ?
In one tutorial I've found the -term function for that but in my case
system didnt suggest me to add new caps
You have to build capping groups onto the termini. See, for instance the [ACE]
and [NME] groups in the .rtp file.
-Justin
James
2011/10/28 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
James Starlight wrote:
Dear Gromacs users!
I've forced with some problem of preparing topology of my input
pdb via pdb2gmx.
My input structure( gramicidin ion chanell) consist of some
heteroatoms due to the presence of the non standart aminoacids
in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L
analogs)
I've tried to parametriesed that structure via different force
fields but in all cases there are not suitable topologies for
that aminoacids
e.g
Fatal error:
Residue 'FOR' not found in residue topology database
How I can solve that problem? I've tried to look for the
suitable itp file but could not find it too :(
For new protein residues, you do not need an .itp file, you need a
suitable .rtp entry such that pdb2gmx can incorporate it into your
topology.
http://www.gromacs.org/__Documentation/How-tos/__Parameterization
<http://www.gromacs.org/Documentation/How-tos/Parameterization>
http://www.gromacs.org/__Documentation/How-tos/Adding___a_Residue_to_a_Force_Field
<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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