GROMACS version:2018.1
GROMACS modification: Yes/No
Here,is the command i put for generating configuration, i had tried umb_sampling tutorial trying to work with mine system which contain,Au+Z9FE(a ligand)+CL,There are 2 identical system which are solvated, i seperated them in a index file with name chain A,chain B and i produced a pores file for one of them by command:
gmx genrestr -f npt.gro -n index.ndx -o posre.itp
then added this file in mine topology as well as 1 ligand.itp file also
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr -maxwarn 1
:-) GROMACS - gmx grompp, 2018.1 (-:
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GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/parul/umb_samp_iiser/trial
Command line:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr -maxwarn 1
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘optimize_fft’
Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’
NOTE 1 [file md_pull.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file md_pull.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Setting the LD random seed to -374099684
Generated 399 of the 1830 non-bonded parameter combinations
ERROR 1 [file top_Z9FE.itp, line 63]:
** moleculetype Z9FE is redefined**
There were 2 notes
Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1469)
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
this error is coming ,why?can u please help me!!!