priya thiyagarajan wrote:
hello sir,
Thanks for your reply.
initially i tried with pdb2gmx command.but i got error.
as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC.
when i performed
pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh
it showed error as
*Processing chain 2 'A' (16 atoms, 1 residues)
Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581
Fatal error:
Residue 'BFC' not found in residue topology database*
i know i want to include BFC residue into my rtp file but dono how to
include.. how can i get those parameter to include like its angles,
dihedrals etc.
x2top ll give top and rtp file.so i tried that.
how to solve my problem.
help me with your answer sir.
Start with the link I already provided and follow the instructions exactly:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Doing so will require a suitable .rtp entry (see the manual), which may also
require you to derive parameters for the species of interest, an expert topic
that may take considerable time to achieve.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
--
========================================
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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