hello every one
I am working on complex with popc membrane i did
perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
after this step minimization
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
i got error
Fatal error:
number of coordinates in coordinate fil
On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
hello every one
I am working on complex with popc membrane i did
perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
after this step minimization
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
i got error
Fatal er
hello gromacs users
ohk justin but if unk is deleted then how to put it back in
system_inflate.gro
On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul wrote:
>
>
> On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
>
>> hello every one
>> I am working on complex with popc membrane i did
>>
>> perl inflategro.pl
hello every one
ohk i havbben pasted UNK portion from old files because it is still missing
in system.gro now after running minimization i got new error old problem
has resolved
:-) grompp (-:
Option Filename Type Description
hello every one
i have been removed all the error of previous output but still i got one
new error
Fatal error:
[ file strong_posre.itp, line 3886 ]:
Atom index (3882) in position_restraints out of bounds (1-3881).
This probably means that you have inserted topology section
"position_restraints"
in
On 7/10/14, 5:44 AM, RINU KHATTRI wrote:
hello every one
i have been removed all the error of previous output but still i got one
new error
Fatal error:
[ file strong_posre.itp, line 3886 ]:
Atom index (3882) in position_restraints out of bounds (1-3881).
This probably means that you have inser
hello gromacs users
thank you justin i got system_shrink.gro after 20 energy minimization and
shrinking next step is solvate your syetem but no command is there the
command is there is
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o system_solv_ions.gro -p top
hello
i am following the lysozyme tutorial
editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0
solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
but after running second command i got error solvate command not found
gmx solvate is also not working
On Fri, J
On 7/11/14, 2:57 AM, RINU KHATTRI wrote:
hello gromacs users
thank you justin i got system_shrink.gro after 20 energy minimization and
shrinking next step is solvate your syetem but no command is there the
command is there is
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
geni
On 7/11/14, 3:18 AM, RINU KHATTRI wrote:
hello
i am following the lysozyme tutorial
editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0
Don't alter the box like this; it's totally nonsensical.
solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
but after r
hello everyone
now i got the minimize structure after addition of water and ions (14 cl-)
i have been select the
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
-nname CL -nn 14
13 th option sol in out put
how can i analyze my structure means is it ok or not because next
st
hello every one
i am working on complex with popc membrane after visualization of minimize
structure (after solvation and addition of ions 14 cl-) in VMD i saw
protein is moving out em.gro from the lipid membrane i dont know how to
resolve it
help
On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI
w
hello gromacs users
i saw in vmd system.gro its little bit ok very small fragment of protein
is out but in shrinkage.gro file box and protein is separated
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#
kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> RINU KHATTRI
> Sent: Wednesday, 16 July 2014 3:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
> not match
>
> hello gromacs users
> i saw in vmd system
half Of
> > RINU KHATTRI
> > Sent: Wednesday, 16 July 2014 3:24 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
> > not match
> >
> > hello gromacs users
> > i saw in vmd system.gro its little
u own is a hammer, every problem begins to resemble
>> a nail.
>>
>>
>> > -Original Message-
>> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
>
On 7/16/14, 6:53 AM, RINU KHATTRI wrote:
hello gromacs users
i am working on protein complex with popc membrane
at the time of minimization and shrinking steps my protein complex is out
of the lipid membrane protein is in the lipid membrane till inflate.gro but
after that it is out
This indic
oun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> RINU KHATTRI
> Sent: Wednesday, 16 July 2014 3:41 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
> not match
>
> hello every one
>
hello gromacs users
i used vmd and both the command pbc box and periodic images in all 6 frames
+X -X +Y -Y +Z -Z and self but this action can not put protein inside the
box
and pbc box action only a box is created around protein and lipid 1/4
protein is in side the box
how to put it in side
kindly
On 7/17/14, 4:52 AM, RINU KHATTRI wrote:
hello gromacs users
i used vmd and both the command pbc box and periodic images in all 6 frames
+X -X +Y -Y +Z -Z and self but this action can not put protein inside the
box
and pbc box action only a box is created around protein and lipid 1/4
protein is
hello gromacs users
i saw my em.log file after minimization no position restrain term is there
even i used -D flag
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef -DSTRONG_POSRES
#include "strong_posre.itp"
#endif
; St
hello justin images can not be sent by this email address (gmx--) i am
helpless how can i send it to you (protein is out side the lipid membrane )
thank you
On Fri, Jul 18, 2014 at 1:01 PM, RINU KHATTRI
wrote:
> hello gromacs users
> i saw my em.log file after minimization no position restrain
hello every one
i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
working even i added DSTRONG_POSERES in topology file
i simpley used DPOSERES it workks in log file value is there
Energies (kJ/mol)
BondG96Bond Angle G96AngleProper Dih
On 7/18/14, 3:34 AM, RINU KHATTRI wrote:
hello justin images can not be sent by this email address (gmx--) i am
helpless how can i send it to you (protein is out side the lipid membrane )
thank you
Upload images to a file-sharing service and post the links to the images.
-Justin
On Fri,
On 7/18/14, 6:38 AM, RINU KHATTRI wrote:
hello every one
i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
working even i added DSTRONG_POSERES in topology file
Because you've made a typo. -DSTRONG_POSERES will not trigger the STRONG_POSRES
block.
-Justin
i sim
hello everyone
ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
and -DSTRONG_POSERES
ok i will try to send the image
kindly check my tolpology is it ok
thanks in advance
On Fri, Jul 18, 2014 at 4:10 PM, Justin Lemkul wrote:
>
>
> On 7/18/14, 3:34 AM, RINU KHATTRI wrote:
>
On 7/19/14, 12:37 AM, RINU KHATTRI wrote:
hello everyone
ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
and -DSTRONG_POSERES
Simply put, that's the wrong syntax. #ifdef statements should not be prefixed
by -D. This is what is correct (and what is specified in the t
hello everyone
i know justin -D is for minim.mdp not for topology i used simply D
still it is not working
kindly help
On 7/19/14, Justin Lemkul wrote:
>
>
> On 7/19/14, 12:37 AM, RINU KHATTRI wrote:
>> hello everyone
>> ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
>> a
On 7/19/14, 9:56 AM, RINU KHATTRI wrote:
hello everyone
i know justin -D is for minim.mdp not for topology i used simply D
That's still wrong. There should be no "D" or "-D" in the #ifdef statement;
it's cpp macro syntax. Please look at the block I provided before:
#ifdef STRONG_POSRES
#
hello everyone
thanks justin it works but problem is at the same place even one more
problem ligand is out side the protein and protein is out side the popc
kindly help
On Sat, Jul 19, 2014 at 7:39 PM, Justin Lemkul wrote:
>
>
> On 7/19/14, 9:56 AM, RINU KHATTRI wrote:
>
>> hello everyone
>>
>>
On 7/21/14, 11:30 AM, RINU KHATTRI wrote:
hello everyone
thanks justin it works but problem is at the same place even one more
problem ligand is out side the protein and protein is out side the popc
So you've placed the ligand incorrectly or otherwise manipulated the coordinates
wrong. Give
hello everyone
ok justin iam sending you the link of images
http://s48.photobucket.com/user/mittukhattri/media/Screenshot-3_zps81b0c070.png.html
http://i48.photobucket.com/albums/f213/mittukhattri/Screenshot-3_zps81b0c070.png
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#en
On 7/23/14, 12:48 AM, RINU KHATTRI wrote:
hello everyone
ok justin iam sending you the link of images
http://s48.photobucket.com/user/mittukhattri/media/Screenshot-3_zps81b0c070.png.html
http://i48.photobucket.com/albums/f213/mittukhattri/Screenshot-3_zps81b0c070.png
Rendering the box vectors
hello everyone
thank you justin but how can i increase the box size i am using the box
vector which is present in popc_whole.gro
how can i edit it
and one more problem when i see it in vmd my ligand is out side the protein
kindly help
On Wed, Jul 23, 2014 at 5:00 PM, Justin Lemkul wrote:
>
>
>
On 7/23/14, 12:12 PM, RINU KHATTRI wrote:
hello everyone
thank you justin but how can i increase the box size i am using the box
vector which is present in popc_whole.gro
how can i edit it
editconf
and one more problem when i see it in vmd my ligand is out side the protein
Position the pr
hello everyone
thank you justin
i did the same
till minimization without the ligand it is in the lipid and center but i
edit the box size arbitrary i used x and y axis as present in popc but in z
axis used 10.0 so there is overlapping of protein and lipid i think
this can create problem
help
On 7/24/14, 11:57 AM, RINU KHATTRI wrote:
hello everyone
thank you justin
i did the same
till minimization without the ligand it is in the lipid and center but i
edit the box size arbitrary i used x and y axis as present in popc but in z
axis used 10.0 so there is overlapping of protein and
hello everyone
i used editconf
editconf -f protein.gro -o protein_newbox.gro -box (membrane box
vectors) -center *x y z*
but in z axis i have been increased box size 10. (previously it is
6.23910 6.17970 6.91950
http://s48.photobucket.com/user/mittukhattri/media/ri_zpsbb51fbd7.png.html?fi
On 7/28/14, 1:42 AM, RINU KHATTRI wrote:
hello everyone
i used editconf
editconf -f protein.gro -o protein_newbox.gro -box (membrane box
vectors) -center *x y z*
but in z axis i have been increased box size 10. (previously it is
6.23910 6.17970 6.91950
http://s48.photobucket.com/user/
hello every one
i am working on complex with popc membrane i got error in Deuterium
Order Parameters group 1 does not have same number of elements as grp
1
i used the command
make_ndx -f md_0_1.tpr -o sn1.ndx
0 System : 38483 atoms
1 Protein : 3873 atoms
2 Protein-H
hello everyone
i have been resolved the problem (del 0-23) all the elements
but in output i got lots of warning
WARNING: distance between atoms 9299 and 9301 > 0.3 nm (0.444934).
Index file might be corrupt.
WARNING: distance between atoms 9351 and 9353 > 0.3 nm (1.707690).
Index file might be corr
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