Emine Deniz Tekin wrote:
Hi gromacs users,
I am using the gromacs 4.5.3 version. I created a lipopetide which
consist of 12 Carbon atoms (tail) connected to
Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I saved it
as a pdb file.
Then, when I used the following command in gromacs:
pdb2gmx –f lipopepArgus.pdb (GROMOS96 45a3 force field&spc type water
model)
I got the following error message:
Fatal error:
Residue 'DEF' 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
As far as I could understand, there is no problem with the residues
but there is a problem with the atoms in the tail (12 Carbon atoms, 23
Hydrogen atoms and an Oxygen atom, actually it is called a lauroic
acid). These atoms are defined as DEF. I thought I should rename the
pdb to the expected name given in the .rtp file of the 45a3 force field
for my lipopeptide. But I could not find a parameterization for the
lauroic acid. In this case, what shoul I do?
At the
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks
page, I found;
*Abbrev.*
*Source*
*2*
*Full Name*
*Formula*
*Specifics*
LAU
fa.itp
O
lauroic acid
C_11 H_23 COOH
-
Does using fa.itp file solve my problem? If yes, where can I get this file?
This topology is from the deprecated Gromos87 (hacked) force field called ffgmx.
Don't use it. The reasons are described in the manual. What's more, you
can't use a standalone topology if your molecule is covalently linked to a
peptide. You can't have bonds between different [moleculetypes] (i.e. between
topologies) in Gromacs.
The proper procedure is to parameterize the lauroic acid:
http://www.gromacs.org/Documentation/How-tos/Parameterization
or obtain compatible parameters from elsewhere and implement them in your chosen
force field:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
You could use Berger lipid parameters for the lauroic acid moiety, you'll just
have to add this residue to the force field. The membrane protein tutorial I
wrote will walk you through how to modify the force field properly.
http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
-Justin
I would be so glad if you can help me solve this problem.
Thank you in advance,
Deniz
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
