Ok,
Thanks a lot!
De: Justin Lemkul
Para: Discussion list for GROMACS users
Enviadas: Segunda-feira, 17 de Dezembro de 2012 12:08
Assunto: Re: [gmx-users] mdp file warnings
On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
> OK, so if i got this right al
OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com? I thought that i had to make a substitution in
one of the existing terms.
Thanks.
De: Justin Lemkul
Para: Eduardo Oliveira ; Discussion list for
Hi,
I'm setting my system but when I run grompp I get a warning and the program
terminates. It says the following:
You are using pressure coupling with absolute position restraints, this will
give artifacts. Use refcoord_scaling option.
I want to try it but i don't know where to change thi
Hi,
I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i
get a fatal error message:
Fatal error:
Incomplete ring in HIS415
The problem is, when I open the structure on pymol i can't see any missing
atoms. Does anybody had the same problem?
Regards,
Eduardo
--
gmx-us
Thanks a lot!
De: Justin Lemkul
Para: Discussion list for GROMACS users
Enviadas: Segunda-feira, 15 de Outubro de 2012 9:42
Assunto: Re: [gmx-users] bonds braking
On 10/15/12 8:40 AM, Eduardo Oliveira wrote:
> Thanks!
>
> So, if i understood
Hi,
I'm having trouble simulating a protein kinase on water. During the simulation,
the molecule moves towards the box limits and some residues apear on the other
side. Almost like they are interacting with water molecules on different sides
of the box. I'm on my third simulation and the proble
Hi all,
I was preparing my system for a simulation and after using grompp i got the
following message:
Fatal error:
Invalid T coupling input: 2 groups, 1 ref_t values and 1 tau_t values
For more information and tips for troubleshooting, please check the GROMACS
for more information here goes th
Ok, thanks again. That actually worked.
De: Justin A. Lemkul
Para: Discussion list for GROMACS users
Enviadas: Terça-feira, 3 de Abril de 2012 18:30
Assunto: Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
> Ok, thanks for the advice and sorry
Ok, thanks for the advice and sorry for sending the attached file.
De: Justin A. Lemkul
Para: Discussion list for GROMACS users
Enviadas: Terça-feira, 3 de Abril de 2012 16:51
Assunto: Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
> Tha
Hi all,
After i ran grompp I've the following message:
Fatal error:
3 atoms are non part of any of the T-coupling groups
It is probably in refference to the 3 CL atoms i've introduced into the system
to neutralize my protein charge. Here are the command lines for genion and
grompp
genion_d -
Hi all,
After a ran grompp_d in prepration for a Steepest Descente Minimizations with
constraints i got the folowing error message:
Fatal error:
No such moleculetype CL-
I don know for shure but i think that i forgot to modify some of the files with
the numbers os CL- ions I've introduced int
Hi all,
I' ve stumbled upon a problem when i used genion to prepare my files. Here's
the comand line:
genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1 -p
sistema.toI
I've got this in return:
Fatal error:
Your solvent group size (73282) is not a multiple of 19.
How to
eyond
the standard index groups. In that case do not use -n in grompp.
On 2012-03-30 05:06:34PM -0700, Eduardo Oliveira wrote:
> Thanks for the quick reply!
>
> Well, i tried to address the index file "indes.ndx" but as you already told
> me the file doesn't exist in t
__
De: Mark Abraham
Para: Discussion list for GROMACS users
Enviadas: Sexta-feira, 30 de Março de 2012 20:42
Assunto: Re: [gmx-users] index.ndx files
On 31/03/2012 10:39 AM, Eduardo Oliveira wrote:
Hi,
>
>
>I'm trying to set up a configuration file to but i keep gettin an e
Hi,
I'm trying to set up a configuration file to but i keep gettin an error after
the grompp_d run. I'm using the command line as follows:
grompp_d -f stpr.mdp -c sistema_boxwater.gro -p sistema.top -o sistema_stpr.tpr
-n
Text in bold correspond to my files.
This is what i got:
File input/
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