[gmx-users] regarding topology

[Justin A. Lemkul]

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

-- 
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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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