James Starlight wrote:
Dear Gromacs users!
I've forced with some problem of preparing topology of my input pdb via
pdb2gmx.
My input structure( gramicidin ion chanell) consist of some heteroatoms
due to the presence of the non standart aminoacids in sequence: FOR,
DLE, DVA, ETA ( this the R isomers instad of L analogs)
I've tried to parametriesed that structure via different force fields
but in all cases there are not suitable topologies for that aminoacids
e.g
Fatal error:
Residue 'FOR' not found in residue topology database
How I can solve that problem? I've tried to look for the suitable itp
file but could not find it too :(
For new protein residues, you do not need an .itp file, you need a suitable .rtp
entry such that pdb2gmx can incorporate it into your topology.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
