[gmx-users] residue not found

[Justin Lemkul]

On 8/8/18 10:09 AM, Soham Sarkar wrote:
> Put your residue name in the residuetypes.dat file and designate it as
> nucleic acid. Keep the same file in your ff folder, which in turn should be
> in the working directory.

That won't solve the issue. The problem is that "THY" is not recognized 
in the force field(s) the OP is trying to use. Consult the .rtp file for 
the actual nomenclature. Most force fields use DT instead of THY, DA for 
(deoxy)ADE, RA for ADE (RNA), etc. AMBER uses special residue names for 
5'- and 3'-nucleotides, as well.

-Justin

> On Wed, 8 Aug 2018, 6:54 pm abhisek Mondal, <abhisek.mndl at gmail.com> wrote:
>
>> Hi,
>> I'm facing a very odd issue in gromacs. I'm trying to execute "pdb2gmx -f
>> dna1.pdb -o dna.gro" using AMBER/CHARMM forcefield, but getting the
>> following error:
>>
>> *Program pdb2gmx, VERSION 4.6.2*
>> *Source code file: /home/user/gromacs-4.6.2/src/kernel/resall.c, line: 642*
>>
>> *Fatal error:*
>> *Residue 'THY' 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>*
>>
>>
>> I'm using DNA first time in gromacs.
>> What should be the residue name instead of the name of the bases I can't
>> understand. A little suggestion would be terrific here.
>>
>> Thank you.
>>
>> --
>> Abhisek Mondal
>>
>> *Senior Research Fellow*
>> *Protein Crystallography Group*
>>
>> *Structural Biology and Bioinformatics Division*
>> *CSIR-Indian Institute of Chemical Biology*
>>
>> *Kolkata 700032*
>>
>> *INDIA*
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================