-h?
>
> Mark
>
>
> On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis
> wrote:
>
> > Hello,
> >
> > Thank you all for your help! I got it working by downloading the
> > executables directly and setting the path but i do get the
> >
> > Progra
Hello,
Thank you all for your help! I got it working by downloading the
executables directly and setting the path but i do get the
Program do_dssp, VERSION 5.0
Source code file:
/home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670
Fatal error:
Failed to execute
Hi,
Thank you for your answer, could you please give me some more info on where
to find them and how to use them for the whole trajectory?
Cheers,
Nicholas
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Hello,
I am trying to do a secondary structure analysis to get the percentages of
each secondary structure in my protein. I know i can use do_dssp but
unfortunately DSSP is not installed on the cluster that i have been using
and i do not have the acess to install it. Any other ways to do it? or
wo
Hello,
I am trying to measure the distances between certain residues over the
course of my simulation. I have created an index with these residues. So
far i have tried using gmx mdmat but since there are only five residues the
resulting map consists of 25 large boxes, of different shades, which is
Sorry, I just have all the commands saved and just copy, paste and
customise according to the files i am using. I used:
grompp -f em-sol-pme.mdp -c solv.gro -p fws.top -o ion.tpr
not fws-b4ion.gro
Thanks,
Nick
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These are the commands i used:
pdb2gmx -ignh -f 3ZK3-etc.pdb -o fws.gro -p fws.top
for the topology and selected my custom AMBER forcefield which i had placed
in the working directory and chose tip3 water
editconf -f fws.gro -o fws-PBC.gro -bt dodecahedron -d 1.2
for the box
gmx solvate -cp fw
I added them manually in the initial fws.gro file and changed the number on
top. If you see the solv.gro file, they are included, along with the
solvent, but for some reason, 42 less solvent atoms are added.
Thanks,
Nicholas
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Hello again,
I am trying to include a ligand in my structure, which consists of 42
atoms, using an .itp file, in the AMBER forcefield. The itp was generated
by antechamber and is the ligand_backup.itp. Everything works fine until I
try to solvate it. It seems that the gro file produced by the solv
FF (Johnny Lu)
>2. Re: Setting Non-bonded Scaling Constant for Amber FF
> (Justin Lemkul)
>3. Re: Iron containing structure simulation crash
> (Nikolaos Michelarakis)
>4. Re: Iron containing structure simulation crash
> (Nikolaos Michelarakis)
>
>An output coordinate file is always produced unless mdrun completely fails
and
>seg faults. That doesn't mean the coordinates are sane. It's meant to
help you
>diagnose in cases like this where you have an absurd force on some atom.
>What is atom 2832? What's around it? Is there anything obvi
Hello again,
I finally managed to introduce the iron into my structure and generate a
topology. However, when i first run the initial energy minimization, either
in vacuum or with solvent, i get the following message:
It stopped because the algorithm tried to make a new step whose size was too
sm
Thanks a lot. Didn't realize that this would affect the topology.
I now get an error that Fe is not in the residuetype.dat file. Since
Gromos96 has parameters for Fe, shouldn't it be in the file? Just wondering.
Thanks again,
Nicholas
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Here are the links:
https://drive.google.com/file/d/0BzqRbRx4Ynf0c28zYVhoY3JRenM/edit?usp=sharing
for the pdb file.
https://drive.google.com/file/d/0BzqRbRx4Ynf0TmNsckliYWtqQUU/edit?usp=sharing
for the topology.
Cheers!
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Hello again,
Since I could not find any reliable parameters for the Fe-O for the GROMOS
96 forcefield I decided to modify it to use the parameters for its Fe-N in
its HEME group. While reading through the gromos54a7 files i saw that it
has parameters for the Fe-O bond so I thought that it might be
Hi Justin,
Thank you for your answer. I was going to use the parameters from an MM
paper but since you mentioned that, any idea where I can find some better
parameters? I don't want them to be perfect and I don't have time for QM,
just something so the protein won't blow up up.
Thanks,
Nicholas
Hello,
I want to run a protein simulation where I will include a ligand which has
an Fe(III) bound on it. So far I have found how to deal with the ligand,
creating its topology seperately and then adding it. Since I am quite new
to MD I have some questions on how to include the Fe(III) and where.
Hello All,
I am trying to simulate a structure containing a licam-4 or licam-5 ligand
with an iron (Fe) bound on it. I was wondering if anyone has any parameters
for this iron?
Thank you very much in advance!
Cheers,
Nicholas
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Hey,
Thanks a lot, I fixed the file but I am now getting a python error, I think.
Traceback (most recent call last):
File "./cgenff_charmm2gmx.py", line 792, in
m.read_mol2_coor_only(mol2_name)
File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only
atomi = int(entry[0])-1
Va
Hello again,
This what I have been trying to do so far. This is the command to run the
script:
./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff
and this is the error I have been getting along with 2 Notes:
NOTE2: Please be sure to use the same version of CGenFF in your
On 23 June 2014 17:42, Justin Lemkul wrote:
>
>
> On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote:
>
>> Dear All,
>>
>> First, I would like to say that I have started using GROMACS during this
>> last month so please take that in mind when answering.
>&g
Dear All,
First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.
I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tungsten metal ion and some other cofactors. I
understand
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