On 1/20/13 3:57 PM, Tom wrote:
Dear Gromacs User
I built DNA with the pdb file and *mol2
But when I used pdb2gmx to obtain *top file, pdb2gmx give error
report when I chose charmm27:
---------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581
Fatal error:
Residue 'T' 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
-------------------------------
Also can not work for the other forcefileds.
Why for simple DNA is so difficult to build topology file?
Your residue names need to match the force field's expectations. That much is
true for any molecule passed to pdb2gmx - protein, DNA, RNA, whatever. Consult
the .rtp file for your chosen force field and edit your coordinate file accordingly.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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