Dear users,
I used genion to neutrilize my system with two Na+ ions.
Now with my new .gro and .top file and with a minimization (mdp) input
file I try to make a .tpr file with grompp in order to minimize my
structure.
When I run grompp I get an error
Program grompp, VERSION 3.3.3
Source code
Dear all,
Thanks for solving lot of problem of me in doing membrane
membrane protein simulation. Now I have a one problem I want to add ion to
the my system by genion command
for this i am following justin's tutorial but in the genion step when i
have put the command like
nitu sharma wrote:
Dear all,
Thanks for solving lot of problem of me in doing
membrane membrane protein simulation. Now I have a one problem I want to
add ion to the my system by genion command
for this i am following justin's tutorial but in the genion step when i
Hi everyone,
I am facing a peculiar problem with genion. I have a system
with overall charge
0f +3.
I want genion to add enough ions to make the cocncentration 10 micromoles/litre.
When I give the command
genion -s em.tpr -o ions.gro -conc 0.1 -pname NA+ -nname CL- -p
sarbani chattopadhyay wrote:
Hi everyone,
I am facing a peculiar problem with genion. I have a
system with overall charge
0f +3.
I want genion to add enough ions to make the cocncentration 10
micromoles/litre.
When I give the command
genion -s em.tpr -o ions.gro -conc
Hi all,
I do have a weird behaviour with genion, which fails with the message:
ftp2fn: No filetype .???
No option -cpo
Segmentation fault
and I can't figure out what I do wrong. I couldn't not find any
reference to it either.
It seems that a file cannot be accessed but I couldn't get in
Hi Gurpreet,
You probably performed energy minimization without a box, without PBC.
Then you generated a box using editconf. That's where the PBC comes
in. With genbox you fill the thing with solvent, and running grompp
then will provide you a run input file, which is set up to be used for
a
Thanks Tsjerk for you reply
i did not get your point . i think you are asking me whether i used PBC or
not , so i want to tell you that the .tpr file which i used for genion
command was created without using PBC.
but will it make any difference ?
Thanks
With Regards
Gurpreet
On 7/16/07, Tsjerk
Thanks Tsjerk
I referred the mail about the broken molecules but there the problem is i
think somewhat different. in that case broken molecules are coming becasue
of the PBC . since PBC is being used that is why some part of the molecule
is coming from the other side of box and its looking as
Hello users,
I am carrying a protein simulation using g43a1 force field in gromacs 3.3
i carried out some intial simulation without water in the absence of the
neutralizing ions
my system was going fine at that time but when i used the genion command to
add ions , i found that my protein was
Hello,
I am facing a problem while trying to neutralize my molecule.
My molecule is a protein and after writing input file[.tpr] on seeing a
charge of 6.0e+ i am trying to neutralize it by using 6 CL- ions. when
i have tried 'genion' for small molecules it was running fine,but for this
C.RAMYA wrote:
Hello,
I am facing a problem while trying to neutralize my molecule.
My molecule is a protein and after writing input file[.tpr] on seeing a
charge of 6.0e+ i am trying to neutralize it by using 6 CL- ions. when
i have tried 'genion' for small molecules it was running
Hi Ramya,
don't forger to search the archive at http://www.gromacs.org/search
before posting. As David said, it looks like that old genion+
gcc4.series compiler problem. (I also had it) Try compiling with
Intel, gcc-3,gcc-2.96.
Have a nice day.
On 6/6/07, David van der Spoel [EMAIL PROTECTED]
hello,
OS is fedora 5
Compiler is cpp
how can this be sorted out??
Thanks.
C.RAMYA wrote:
Hello,
I am facing a problem while trying to neutralize my molecule.
My molecule is a protein and after writing input file[.tpr] on seeing a
charge of 6.0e+ i am trying to neutralize
C.RAMYA wrote:
hello,
OS is fedora 5
Compiler is cpp
how can this be sorted out??
gcc -v
if it says 4.1.x your machine is affected and you need to get another
compiler or use the cvs 3.3 release code.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
C.RAMYA wrote:
hello,
OS is fedora 5
Compiler is cpp
cpp is a pre-processor http://en.wikipedia.org/wiki/C_preprocessor, not
a compiler.
Mark
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OZGE ENGIN wrote:
Hi gromacs-users,
I have a problem with the simulation of a capped lysine residue.I followed the
tutorial step by step. I added 1 Cl ion into my system in order to neutralize
the overall charge by using genion, and then used the grompp command and I
encountered with the
Hi gromacs-users,
I have a problem with the simulation of a capped lysine residue.I followed the
tutorial step by step. I added 1 Cl ion into my system in order to neutralize
the overall charge by using genion, and then used the grompp command and I
encountered with the following error:
OZGE ENGIN wrote:
Hi gromacs-users,
I have a problem with the simulation of a capped lysine residue.I followed the
tutorial step by step. I added 1 Cl ion into my system in order to neutralize
the overall charge by using genion, and then used the grompp command and I
encountered with the
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and
it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it
might be my system, so went to /tutor/speptide, but it was the same behaviour.
I am using gromacs 3.3.1. As I recall genion worked fine
Abil Aliev wrote:
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with
Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na.
I thought it might be my system, so went to /tutor/speptide, but it was
the same behaviour. I am using gromacs 3.3.1. As I recall
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na
and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I
thought it might be my system, so went to /tutor/speptide, but it was the
same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine
No, i am not. you?
On a serious note, bug 108 that David referred to (last modified this morning)
suggests compilaton problems with gcc4 due to pbc.c, which doesnt sound healthy.
The same bugzilla page has a possible cure with suggestion to use gcc3, but
changing from one gcc to another is
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