[gmx-users] regarding rtp file

[Justin A. Lemkul]

priya thiyagarajan wrote:
> hello sir,
>  Thanks for your reply..
> As you suggest i tried with all available forcefield for my lipopeptide 
> but i am getting the same error,,
> 

I have posted this link several times before:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

All the necessary steps are spelled out there.  There is no force field that 
will contain the residue you seek; you have to add it yourself.

> 
> *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.

The error message tells you exactly what is wrong (in this case, not completing 
step #5 in the link above).

> 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
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------*
> 

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Also, a result of not completing step #1 in the "adding a residue" link above.

> 
> since mine is connected cyclic lipopeptide even i cant try using  prodrg 
> server too.
> i dono how to generate my topology  file.
> pls help me with your answer.

I've tried and at this point am repeating myself.  Also note that there are 
numerous posts in the list archive about dealing with cyclic peptides (which are 
not trivial).  I would suggest you search for them.  You should also simplify 
your system until you understand the workflow.  Deal with a custom residue in a 
normal linear peptide, then introduce the cyclic peptide and the issues it may 
present.

-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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