Jack Shultz wrote:
Hello,
I am experimenting with formatting pdb files using pdb2gmx. Currently
I am downloading ligand files from RCSB.ORG. These are non-protein pdb
files. When I look at their residues, instead of having a standard
residue, they use their pdb id as the residue id. pdb2gmx does not
like this because these are not standard residues. Is there a setting
I can use to make pdb2gmx to ignore this? Otherwise I can use a sed
command to replace all instances of a given residue name. However,
when I try replacing with a standard residue name, I still run into
errors.
Even if you could make pdb2gmx ignore the given residue name, it has to know
what molecule you have in order to construct the topology. Usually such a
procedure does not work for ligands.
Here is an example ligand pdb file
http://www.rcsb.org/pdb/files/ligand/002_ideal.pdb
Notice instead of having a standard residue it uses 002
ATOM 1 C1 002 A 1 -1.036 0.293 0.447 1.00 10.00 C
ATOM 2 C2 002 A 1 -1.041 1.804 0.685 1.00 10.00 C
ATOM 3 C3 002 A 1 -2.288 2.191 1.482 1.00 10.00 C
....
Any advice? Does GROMACS only support the standard 20 amino acids?
Check the .rtp file for the force field you're trying to use. You can only use
pdb2gmx if the appropriate building block is present (primarily amino acids and
nucleotides).
You can build a topology using the PRODRG (beta) server, but do note that the
charges and charge groups will require manual adjustment and validation. Hence
why parameterization is difficult!
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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