In the old version of gmx, and I think nobody changed a single line of
code, this is the message you would get regardless of the file you input.
Buggy, yes. Check the mailing list, check the code yourself, as you love
to say.
Guillem
>
>> Opening file pull1.pdo.gz.
>> --
> Thanks Mark for your advice
>
> I tried to run the simulation even by removing all the restraints as you
> told but the same problem was coming.
> In your second reply you asked me to check the topology file. I have a
> doubt in that, actually what are the things i should look at in the
> topol
Mark Abraham wrote:
Thanks Mark for your advice
I tried to run the simulation even by removing all the restraints as you
told but the same problem was coming.
In your second reply you asked me to check the topology file. I have a
doubt in that, actually what are the things i should look at in
Thanks for the advice
In my case no problem is coming while running the grompp, no warning is
coming. i could able to generate .tpr file without any error.
problem cames only while running the minimization using the .tpr file
For convenience, as mention earlier, following was the problem :
..
Dear gmx users,
Dear Mark thank you very much for your suggestion. I
would like to do MD simulation at perticular pH. I think that in AMBER it is
possible but I have some problems regarding lipid bilayer parameters. Because
of this I would like to convert gromacs lipid
Please keep conversations on the list in case others want to contribute,
and so the outcomes are stored for others to search for.
I thought I answered your current question when I observed that the
deviations you observe seem normal. The size of these deviations will
depend on the nature of your s
> Dear gmx users,
> Dear Mark thank you very much for your
> suggestion. I would like to do MD simulation at
> perticular pH.
This requires an implicit solvent model, which GROMACS doesn't do, and so
no force field for GROMACS is fit to work with an implicit solvent model
gurpreet singh wrote:
Thanks for the advice
In my case no problem is coming while running the grompp, no warning is
coming. i could able to generate .tpr file without any error.
problem cames only while running the minimization using the .tpr file
For convenience, as mention earlier, following
Dear gmx users,
I built POPE+POPG (total 128 lipid molecules)
lipid bilayer in 3:1 ratio. POPE has neutral charge
and POPG has one unit of negative charge.To this lipid
molecules 3941 water molecules are added.
While creating bilayer.tpr file, it is giving non-zero
total c
Dear Mark,
The problem is a little bit more complicated. I want to build topologies for
dozens of non-peptide inhibitor prototypes using OPLS FF. Thus, if there is a
way to build this by an automatic procedure it would save much time.
Thanks anyway,
Bruno.
> Dear Mark,
>
> The problem is a little bit more complicated. I want to build topologies
> for
> dozens of non-peptide inhibitor prototypes using OPLS FF. Thus, if there
> is a
> way to build this by an automatic procedure it would save much time.
Well, if there was one, I might have mentioned it
> Dear gmx users,
>
> I built POPE+POPG (total 128 lipid molecules)
> lipid bilayer in 3:1 ratio. POPE has neutral charge
> and POPG has one unit of negative charge.To this lipid
> molecules 3941 water molecules are added.
> While creating bilayer.tpr file, it is giving non-zero
> total cha
Hi,
I want to automate the process of getting the index groups in an analysis
program I'm working on.
This is justified because of the large number of groups I work with (more
than 100).
The program asks for user input ("Select a group:") by the function:
void get_index(t_atoms *atoms, char *fn
Hi,
There are a couple of programs out there (e.g. Macromodel) that tries
to do this, even for OPLS, but they fail miserably way too
frequently. I've even seen cases where the autogenerated topology was
reported as "likely high quality", but the small molecule didn't even
have unit charge
> Hi,
>
> I want to automate the process of getting the index groups in an analysis
> program I'm working on.
> This is justified because of the large number of groups I work with (more
> than 100).
>
> The program asks for user input ("Select a group:") by the function:
>
> void get_index(t_atoms
Erik Lindahl wrote:
Hi,
There are a couple of programs out there (e.g. Macromodel) that tries to
do this, even for OPLS, but they fail miserably way too frequently. I've
even seen cases where the autogenerated topology was reported as "likely
high quality", but the small molecule didn't even
Dear Gromacs Users,
Sorry for the repeated question, but I have some problems with ARGN.
If I use ARGN in to PDB, pdb2gmx return this error:
"[...]
Source Code file: pgutil.c, line: 87
Fatal error:
Atom NZ not found in residue 2 while adding improper"
The residue 2 is an Arginine.
The NZ atom
Roberto Marchese wrote:
Dear Gromacs Users,
Sorry for the repeated question, but I have some problems with ARGN.
If I use ARGN in to PDB, pdb2gmx return this error:
"[...]
Source Code file: pgutil.c, line: 87
Fatal error:
Atom NZ not found in residue 2 while adding improper"
The residue 2 is
On 7/4/2007 4:56 PM, Mark Abraham wrote:
Please keep conversations on the list in case others want to contribute,
and so the outcomes are stored for others to search for.
I thought I answered your current question when I observed that the
deviations you observe seem normal. The size of these dev
Thank you, Mark, for your suggestion (even added it to my "favourites").
But in this problem I'd prefer to stick to C, despite the grater difficulty.
Regards,
Pedro.
2007/7/4, Mark Abraham <[EMAIL PROTECTED]>:
> Hi,
>
> I want to automate the process of getting the index groups in an
analysi
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote:
Thank you, Mark, for your suggestion (even added it to my "favourites").
But in this problem I'd prefer to stick to C, despite the grater difficulty.
Regards,
you can of course change the program, but it is absolutely not
necessary. m
Thanks for your comments (and sorry for the late answer)
Actually, I was not primarily thinking about using OpenMosix to run
simulation (that would be stupid considering the size of our cluster).
But it could be valuable to have a tool like OpenMosix when you quickly
want to setup a system (i.
you can of course change the program, but it is absolutely not
necessary. make_ndx will do everything that you need. you don't describe
what you want to do however, therefore we can not help you.
Yes, I described :
"I want to automate the process of getting the index groups in an analysis
pro
Hi Nagaraju (and Mark),
The pH is not defined for a single molecule (protein). The pH and the
pKa values of the side chains couple to the actual protonation states
by probabilities, ergo statistical distributions. You can set up a
simulation according to some reference pH in relation to the pKa
v
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote:
you can of course change the program, but it is absolutely not
necessary. make_ndx will do everything that you need. you don't
describe
what you want to do however, therefore we can not help you.
Yes, I described :
"I want
echo 3 4 5 6 7 | program
I said many index groups.
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Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote:
echo 3 4 5 6 7 | program
I said many index groups.
sure, but then you can generate the input to the program with a script.
that is much more flexible than writing a C program. but it's up to you
of course.
--
>>
>> echo 3 4 5 6 7 | program
>>
>> I said many index groups.
Yeah, we're not stupid, but you're trying to get our help for free... so
give us an example so that we know what's going on in your head!
Mark
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Hi,
I am trying to generate a .tpr file for my ligand and I am
getting the follwing error message.I would be greatful if
somebody could look into it and tell me what the errors
are.Thanks
[EMAIL PROTECTED]:~/gromacs/drugenz2/junk> grompp -f em.mdp -c
trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr -n
> Hi,
>
> I am trying to generate a .tpr file for my ligand and I am
> getting the follwing error message.I would be greatful if
> somebody could look into it and tell me what the errors
> are.Thanks
I'd be grateful if someone did my work too! :-) In particular, what didn't
you understand?
Mark
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