OK, thank you very much.
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May I ask you to share the content of your m2p?
The problem here is that using defaults (no -di) I at least can see some eps
image via evince for example, but when I use m2p consisting of these 2
lines:
xbox = 0.2 ; x-size of a matrix element
ybox
But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?
I used the m2p from the example and tried to change some parameters to take
a look what happens, but I can't see any image at all now :-(
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OK, thank you, now it is clear.
So, that's what I've done so far:
1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving an error on a wrong ELF
descriptor) I i
Thank you Justin, but I am afraid I do not understand what you mean.
I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command line argument. So I suppose,
4.5 can't do
And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.
Or do I missing something? Just in case, here is my command:
$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc
where:
.tpr - after I extended the product tun a couple of times
.xtc - uncha
No, it is there:
$ cd /usr/local/bin
[user@localhost bin]$ ls
dssp vmd
And I had made it executable with chmod a+x
Thank you.
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OK, thanks a lot, got it.
But suddenly I got an unexpected error executing do_dssp:
Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddKypQH4 ddgk6w8G >
/dev/null
Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)
Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...
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Hi,
Hi, I have a rather odd problem running do_dssp:
$ do_dssp -h
bash: do_dssp: command not found
I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.
DSSP is also installed and should be OK:
$ dssp -h
DSSP 2.0.4 options:
-h [ --help ] Display help message
Oh, forgot about it completely... Thank you very much!
BTW, is there any automated way to get rid of solvent molecules in PDB? I
just need the structure for further manipulations (like mutations and adding
several residues to the end). I do not find any options in editconf,
deleting manually from
Hi,
I bumped into a small problem, I think I missed something... so I am asking
for help.
I made a simulation of a protein in water (35ns, extended 3 times from
initial 10ns) and now I need to get a resulting protein structure in pdb.
So I issued:
g_trjconv -s md_input_extended_to35ns.tpr -f md_
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some advice...
I need to simulate a relatively short protein (170aa) in water. No
structures are available for it, so I used a Modeller web server to get
some. Un
Justin Lemkul wrote
> Depends on the algorithm. Pressure is a fickle metric (see
> http://www.gromacs.org/Documentation/Terminology/Pressure and previous
> discussions on this list). It is generally advisable to run equilibration
> using weak coupling (i.e. Berendsen) methods, then switch to a mo
Could it be, say, because of still big conformational changes of the protein?
The size of the system is not that small: the protein is hydrated with 10921
water molecules.
What are the variations of pressure and density that could be tolerated at
this step?
Thank you.
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Hi,
I am trying to simulate a short protein (160aa) in water and after 500ps NPT
equilibration I got rather high value for density: average is 1014 and
pretty stable around this value, but quite noisy (peaks 1010-1020).
Also the pressure is very noisy with average about -7 (I am not sure it is
tha
OK, so there are a lot of necessary dependencies in the command...
Thank you.
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Justin Lemkul wrote
> If you don't specify an actual file name to -s, then all Gromacs tools
> look for a default file name, which in this case is "topol.tpr." Since
> you've run a simulation, clearly you have a .tpr file, which is what you
> need to provide to -s.
I have only one .tpr file - the
Justin Lemkul wrote
> You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
> mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program g_trjconv, VERSION 4.5.5
Source code file: /build
Hi,
I have a general question on cutoff values.
I am using an AMBER03 ff and in a number of papers/tutorials the cutoffs for
vdw/coulomb are reported as low as 0.8 (and up to 1.2 - 1.4 depending on the
interaction type). As far as I understand, increasing this value a bit will
not harm unless ther
Justin Lemkul wrote
> It is calculated correctly, the math is just a bit more complex (see the
> manual for the equations). The distance to the box edge is defined the
> same way, but the two approaches don't necessarily give equally suitable
> results. Consider the first case, which produces a r
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
> In almost all cases, a dodecahedral box is the optimal choice. A cubic
> box with the same periodic distance for an elongated protein would be much
> larger.
OK, got it.
Justin Lemkul wrote
> In the absence of the actual editcon
Hi,
I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered globular enough to try dodecahedron box?
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