i did it but i get this error again.
Sent from my iPad
> On Sep 25, 2014, at 19:29, Justin Lemkul wrote:
>
>
>
>> On 9/25/14 9:56 AM, Yaser Hosseini wrote:
>> hi gromacs users
>>
>> i got this error what can i do??
>>
>> Program pdb2gmx,
thank you for replay
when i want to download this file and i click on it its nothing happend and
just the text page opend and its nothing to download.
Sent from my iPad
> On Sep 26, 2014, at 19:56, Justin Lemkul wrote:
>
>
>
>> On 9/26/14 12:23 PM, Yaser Hosseini wr
thank you i did it.
Sent from my iPad
> On Sep 26, 2014, at 23:42, Justin Lemkul wrote:
>
>
>
>> On 9/26/14 12:50 PM, yaser wrote:
>> thank you for replay
>>
>> when i want to download this file and i click on it its nothing happend and
>> j
hi
i tried add Mn in .itp file but its need some information such as sigma and
epsilon and i search for find this but i cant find this parameters .anyone
knows any things about how can i add Mn in .itp file and if you know any
tutorials articles about add ions .
thanke you.
Sent from my iPho
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
Command 'gcx' from package 'gcx' (universe)
Comm
hi gromacs users
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hi gromacs users
i got this error what can i do??
Program pdb2gmx, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/futil.c, line: 593
File input/output error:
1AKI.pdb
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs
hi gromacs users
i wanted to run this command :
grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
but i dont have this file in my folder path:
ions.mdp
how can i get this file in my path.
thank you.
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thanks.
On 9/25/14, Yaser Hosseini wrote:
> hi gromacs users
>
> i wanted to run this command :
>
> grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
>
> but i dont have this file in my folder path:
>
> ions.mdp
>
> how can i get this file in my path.
&
i dont know how can create ions.mdp file for grompp command in gromacs .
where can i found it??
On Thursday, September 25, 2014 11:14 PM, Justin Lemkul wrote:
On 9/25/14 2:15 PM, yaser wrote:
> i did it but i get this error again.
>
If the file is, in fact in the working directo
hi gromacs user
i have problem with grompp command in gromacs i cant find .mdp files
and i cant pass step 4 in this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html
im new in gromacs please help me to find a way to fix my problems.
thank
hi gromacs users
when i want to run pdb2gmx command i got a fatal error that said :
the residue from MN has lost.
and i used all of force feild but i got this error how can i fix it and
which one of force feild coomand can i use??
thanke you.
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hi
Reading file md.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
which is better)
how can i use this features for better mdrun speed.
thanke you.
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hi gromacs users
i want to run Protein-Ligand Complex but when i want to run this command :
mdrun -deffnm nvt
i got this error
Fatal error:
4 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This
hi
i just want to run
mdrun -v deffnm nvt
i run every command in this tutorials
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html
but at the end i got two errors :
There are: 247500 Atoms
Charge group distribution at step 0: 20986 20508 20732 20838
hi gromacs users
i got error in step four in protein-ligand complex how can i fix it:
Fatal error:
number of coordinates in coordinate file (solv.gro, 144131)
does not match topology (topol.top, 144171)
when i want to ran this:
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
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> Today's Topics:
>
>1. fatal erroe in prorein-ligand comlex (Yaser Hosseini)
>2. Re: fatal er
hi
i want use the amber force field and its need acpype but i got error :
acpype -i ref-ligandChimera.mol2 -c user
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2014-08-27 18:33:08Z Rev:
7828 (c) 2
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