Re: [gmx-users] Problem using gromacs

2016-01-04 Thread shagun krishna
Since you have added the co-ordinayes of jz4 into the CONF.GRO. Therefore to reflect this change you have to increment the second line of conf.gro so that it shows total atoms of the system means protein+ ligand. On Mon, Jan 4, 2016 at 2:57 PM, soumi wrote: > Respected

Re: [gmx-users] Problem using gromacs

2016-01-04 Thread Justin Lemkul
On 1/4/16 4:27 AM, soumi wrote: Respected Sir, I am new user of gromacs. When I use the following command gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr I get the following error :Number of coordinates in coordinate file does not match topology file. Please

[gmx-users] Problem using gromacs

2016-01-04 Thread soumi
Respected Sir, I am new user of gromacs. When I use the following command gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr I get the following error :Number of coordinates in coordinate file does not match topology file. Please tell me how can I correct the number

Re: [gmx-users] Problem using gromacs

2016-01-04 Thread masoud keramati
in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting! On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul wrote: > > > On 1/4/16 4:27 AM, soumi wrote: > >> Respected Sir, >>I am new user of gromacs.

Re: [gmx-users] Problem using gromacs

2016-01-04 Thread Justin Lemkul
On 1/4/16 8:20 AM, masoud keramati wrote: in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting! This comment makes no sense. Changing water models (presumably that is what you mean, and just typoed it) will not work unless