[gmx-users] T-Coupling group Protein has fewer than 10% of the atoms

[David van der Spoel]

akalabya bissoyi wrote:
> hello everybody
> i am trying to setup the position restrained dynamics
>  but failed to proceed,-
> 
> in  terminal window it shows the massage-
> 
> calling /usr/bin/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> turning all bonds into constraints...
> Excluding 3 bonded neighbours for UNK 1
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 44524
> turning all bonds into constraints...
> Excluding 1 bonded neighbours for Cl 16
> turning all bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> Reading position restraint coords from god_b4em.pdb
> renumbering atomtypes...
> converting bonded parameters...
> #     ANGLES:   6075
> #      PDIHS:   2098
> #      IDIHS:   2246
> #       LJ14:   7545
> #     POSRES:   3088
> #     CONSTR:   4142
> #     SETTLE:   44524
> Walking down the molecule graph to make shake-blocks
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> There are: 44541      OTHER residues
> There are:   396    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> WARNING 1 [file aminoacids.dat, line 1]:
>   T-Coupling group Protein has fewer than 10% of the atoms (4007 out of
>   137634)
>   Maybe you want to try Protein and Non-Protein instead?
> Making dummy/rest group for Acceleration containing 137634 elements
> Making dummy/rest group for Freeze containing 137634 elements
> Making dummy/rest group for Energy Mon. containing 55 elements
> Making dummy/rest group for VCM containing 137634 elements
> Number of degrees of freedom in T-Coupling group Protein is 7921.91
> Number of degrees of freedom in T-Coupling group Non-Protein is 267263.09
> Making dummy/rest group for User1 containing 137634 elements
> Making dummy/rest group for User2 containing 137634 elements
> Making dummy/rest group for XTC containing 137634 elements
> Making dummy/rest group for Or. Res. Fit containing 137634 elements
> Making dummy/rest group for QMMM containing 137634 elements
> T-Coupling       has 2 element(s): Protein Non-Protein
> Energy Mon.      has 3 element(s): Protein SOL rest
> Acceleration     has 1 element(s): rest
> Freeze           has 1 element(s): rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): rest
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> writing run input file...
> 
> Back Off! I just backed up pr.tpr to ./#pr.tpr.2#
> 
> There was 1 warning
> 
> gcq#194: "You Crashed Into the Swamps" (Silicon Graphics)
> 
> root at bioinfo-desktop:/usr/local/gromacs/god2# nohup mdrun -deffnm pr &
> [1] 6846
> nohup: ignoring input and appending output to `nohup.out'
> 
> 
> any body can recognize the error,i am attaching the pr.mdp file.
> 

It's just a warning.
It seems though that you have an enormous amount of water for such a 
small protein, you can probably reduce it by at least half (uless your 
protein is completely unfolded).

Please check wiki.gromacs.org for info on temperature coupling.

> Thank you have nice day.
> 
>  AKALABYA BISSOYI
> NIT ROURKELA,INDIA
> 
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se