Hi Dhananjay,
Happy new year :)
Just what it says: not enough ref_t and tau_t values. You use
"Protein" and "Sol" as temperature coupling groups, but likely, you
also have ions in your system, which are not coupled now. You may want
to use "Protein" and "Non-Protein" in stead. In case you have some non
standard groups (modified amino acid, ligands, cofactors), you need to
use an index group. Do not think of giving a cofactor/ligand/small
group of ions a private heat bath. Check the archives using "Not
enough ref_t and tau_t values" as search string, or simply ref_t and
tau_t. You should've done that before posting, really, because this
issue has been dealt with several times already, including
explanations of why not giving private heat baths.
Cheers,
Tsjerk
On 1/2/07, Dhananjay <[EMAIL PROTECTED]> wrote:
Hello all,
I have minimized the pdb file and wish to do mdrun for position restrain
dynamics.
For this when I run grompp programm, it is showing error as follows. I don't
understand why it is showing this error:
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from 2HT1_b4pr.gro
renumbering atomtypes...
converting bonded parameters...
# G96ANGLES: 9382
# PDIHS: 3544
# IDIHS: 2984
# LJ14: 10898
# POSRES: 5054
# CONSTR: 6472
# SETTLE: 25639
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat
There are: 25641 OTHER residues
There are: 648 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 10 elements
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131
Fatal error:
Not enough ref_t and tau_t values!
-------------------------------------------------------
"I was detained, I was restrained" (The Smiths)
Please anybody tell me what is wrong here ?
for the reference I have attached pr.mdp file
Thanking you in advance......
-- Dhananjay
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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