Hi Justin,
The simulation is running fine for this task.
There's something additional I want to do and I'd like to know how you'd
approach it. I want to add charges to each of the protein so that I can
observe how the respective protein interacts with their respective charge
cloud. The proteins
Hi Justin,
The simulation is running fine for this task. Thank you for helping me
There's something additional I want to do and I'd like to know how you'd
approach it. I want to add charges to each of the protein so that I can
observe how the respective protein interacts with their respective
On 8/5/13 5:39 AM, chinnu657 wrote:
Hi Justin,
The simulation is running fine for this task. Thank you for helping me
There's something additional I want to do and I'd like to know how you'd
approach it. I want to add charges to each of the protein so that I can
observe how the respective
oh, sorry.
So the error is:
Fatal error:
Topology include file posre.itp not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
My
On 8/2/13 5:57 AM, chinnu657 wrote:
oh, sorry.
So the error is:
Fatal error:
Topology include file posre.itp not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
There are probably #include statements
Hi Justin,
Yes that was a problem. So after modifying my #include statement in the itp
file (initially top. file), it became:
; Include Position restraint file
#ifdef POSRES
#include posre_2CDS.itp
#endif
thank you
Chinnu
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Thanks Justin. So, I've understood how to calculate the number of
coordinates. That in the topology file matches the amount I calculated (as
per how you just taught me).
I want to put 2 proteins in the same box. I did this by changing the
topology files of the respective proteins to itp. Then a
On 7/31/13 10:07 AM, chinnu657 wrote:
Thanks Justin. So, I've understood how to calculate the number of
coordinates. That in the topology file matches the amount I calculated (as
per how you just taught me).
I want to put 2 proteins in the same box. I did this by changing the
topology files
Hi Justin,
Oh, I see. I am going to paste my commands here.
pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0
cat conf1.gro conf2.gro
On 7/31/13 11:29 AM, chinnu657 wrote:
Hi Justin,
Oh, I see. I am going to paste my commands here.
pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
editconf -f 2CDS_conf.gro -o
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro
topol_1AKI.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp
topol_2CDS.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp
I get the feeling you're not going to be able to see the
On 7/31/13 11:59 AM, chinnu657 wrote:
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro
topol_1AKI.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp
topol_2CDS.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp
I get the feeling you're
Thank you very much Justin. It's working fine now :)
Really appreciate it.
Chinnu
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I actually have another problem. When doing my grompp for nvt equilibration,
I egt the error, Topology include file posre.itp not found. In my topology
file I wrote this:
;Include the force field
#include oplsaa.ff/forcefield.itp
; Include chain topologies
#include topol_1AKI.itp
#include
On 7/31/13 2:48 PM, chinnu657 wrote:
I actually have another problem. When doing my grompp for nvt equilibration,
I egt the error, Topology include file posre.itp not found. In my topology
file I wrote this:
;Include the force field
#include oplsaa.ff/forcefield.itp
; Include chain
Right, I've understood that now. I've altered all of that.
But somehow, the same error message still appears..
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On 7/31/13 3:10 PM, chinnu657 wrote:
Right, I've understood that now. I've altered all of that.
But somehow, the same error message still appears..
Without the command issued, exact error message (copied and pasted from the
terminal), and relevant topology snippet, there's nothing anyone
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