Re: [gmx-users] linking error while trying to build gromacs

[Mark Abraham]

Hi,

The simplest explanation would be that your C compiler and your C++
compiler are somehow incompatible. But we'd have to see eg the terminal log
from cmake to know.

Mark

On Thu, 2 Mar 2017 22:44 Andrey Tolstov  wrote:

> Hello!
>
> I'm trying to install gromacs 5.1.4 on my Ubuntu 16.04. I've unpacked
> sources, made build dir, launched from it "cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DGMX_DOUBLE=off" - it worked fine,
> then ran "make". Compilation was ok, but linker returned an error
> "collect2: error: ld returned 1 exit status" and a lot of undefined
> references, like that:
>
> [ 98%] Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single'
>
> After that I've tried to build and use fftw3, switch from avx to sse4.1,
> switch from gcc-5 to gcc-4.9, but these (or very similar) errors didn't
> disappear. Also I've tried gromacs versions 5.1.3 and 5.0.4 but I've got
> the same problem.
> For more information see the full make log by link
> http://pastebin.com/UeyfPdgA or tail of it with all the errors in
> attached file.
> Can you please help me finding the reason of this problem?
>
> Thanks in advance,
> Andrey
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Re: [gmx-users] force application group wise

[Mark Abraham]

Hi,

This is what pull groups do in GROMACS.

Mark

On Fri, 24 Feb 2017 14:37 Rana Ali  wrote:

> Dear users
>
> We were running MD system consists of ion and water through a nanotube
> under a pressure gradient.
> For that we are applying pressure in terms of force to the molecules.
> Could any body help how to create group so that the external force will be
> applied only on water molecules not on the ions. means how to define the
> force in the .mdp file
>
> Thanks in advance
>
> Warm regards
>
> Rana
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Re: [gmx-users] Simulation crashes: issue with [pair] potential

[Mark Abraham]

Hi,

When you're using a version of the software that's more than three years
old, and a bug was fixed less than two years ago, you need to get an
updated version :-)

Once you do, your problem reduces to whether you can identify few enough
groups of atoms whose pairwise group-group interatomic interactions have
the same shape. They can use the same tables. Trying to use a different
table for eg each atom pair would run out of energy groups, and be an utter
disaster for performance.

Mark

On Wed, 1 Mar 2017 10:18  wrote:

> Dear Mark,
>
> thanks for your comment regarding the pairs interaction. I did know about
> the tabulated choice for nb interaction, but the number of interaction
> will reach more than >200 pair. Even though, I go for the energy group
> description it will need a larger number of groups, as each entry will be
> assigned to one pair (i,j) with i and j index of particles. I have a
> Martini ff underneath, and sure I have several Martini types which reflect
> the amino acid character: (P)Polar, (A)Apolar, (I)Intermediate Polar and
> (C)Charge and in each different types(Qda,Nda,P1,P5,etc). If I use groups
> with P,A,I and C, then the issue will be, that I need to define
> interactions between four groups to describe specific interaction between
> CA atoms in each group.
>
> For instance,
> pair 1 and 34: involves groups (C)-(I) with types Qda and Nda
> pair 1 and 36: involves groups (C)-(I) with types Qda and Nda.
>
> the issue comes that one may need to use different sigmas which are
> defined by the distance between the pairs.
>
> The other pairs are also non-redundant due to atom indexes and different
> sigma parameters which are defined by the distance as well.
>
> Recenlty, I found another choice the [pairs_nb]. Guess you had a comment
> in the past regarding a deprecate directive see at
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097965.html
>
> Currently, I have problem to set it up. Look at a piece of my .itp file
>
> [pairs_nb ]
> 134  1  0.0 0.0  0.34962  0.00974
> 136  1  0.0 0.0  0.29890  0.00712
>
> with error:
> 
> Generated 0 of the 780 non-bonded parameter combinations
> case: 20
> ---
> Program grompp_mpi, VERSION 4.6.5
> Source code file:
> /home/HDD3000/HOME_poma/poma/Software/gromacs-4.6.5/src/gmxlib/gmx_fatal.c,
> line: 597
>
> Fatal error:
> Invalid case in switch statement, file
> /home/HDD3000/HOME_poma/poma/Software/gromacs-4.6.5/src/kernel/topio.c,
> line 1007
> 
>
> initially I used [pairs] without the zeros entries for  qi, qj and the
> last two terms are combination rules for V** and W** parameters. It worked
> as the system was in the minimum energy state (folded state). Now I
> started the simulation in the unfolded state and the distance between
> pairs may reach lengths longer than molecular cutoff. This is the reason
> why I do want to shift the pairs in context of non-bonded picture. Any
> insights will be highly appreciated, maybe I really miss the concept of
> the tabulate scheme & groups definition.
>
> best,
>
> Adolfo
> > Hi,
> >
> > Tabulated non-bonded potentials are possible (see manual), but currently
> > only implemented between pairs of energy groups, and only in the group
> > cut-off scheme. So by e.g. putting each type of particle in its own
> energy
> > group you can arrange for whatever inter-group interactions suit you. But
> > there's only a small number of groups possible, maybe 64 or 128? I
> forget.
> >
> > Mark
> >
> > On Tue, Feb 28, 2017 at 10:22 AM  wrote:
> >
> >> Hi,
> >> We had employed the pair potentials in unconventional way.  They were
> >> used
> >> to describe nonbonded specific Lennard Jones (LJ) Potential between a
> >> pair
> >> of particles. Each pair has a different set of sigma's parameters, but
> >> just one epsilon. Although they are LJ potentials, they are considered
> >> as
> >> bonded interactions by definition and a table is made internally. When
> >> bonded interactions exceed the minimum convention image distance (MCID),
> >> then the simulation generally crashes due to a distance which is above
> >> the
> >> MCID.
> >> Obviously, Gromacs starts complaining about this issue with a warning
> >> regarding a distance between two atoms which is reasonably large and it
> >> assumes that we are performing a free energy calculation. Has anybody
> >> encounter a similar issue before, honestly I would like to find another
> >> way to define the interaction between pair of particles as purely
> >> nonbonded potential (with different sigma's parameters) and not as
> >> pairs,
> >> any help will be appreciate!
> >>
> >> kind regards,
> >>
> >>
> >>
> >> --
> >> Dr. Adolfo Poma
> >> Institute of Physics
> >> Polish Academy of Science
> >> Al. Lotnikow 32/48,
> >> 02-668 Warsaw, Poland
> >>
> >> --
> >> Grom

Re: [gmx-users] Velocity as a function of distance Z (Mark Abraham)

[Mark Abraham]

Hi,

On Wed, 1 Mar 2017 14:11 Kamps, M.  wrote:

Dear Mark,

Thanks again for your reply. I'm sorry for asking these probably
stupid questions, but I'm not able to figure it out.

The objects I am interested in are small polymers, consisting of three
residue groups; Eth EthE and EthB (corresponding to both the end
groups of a polymer, and the middle section). I total these groups
consist of around 25000 atoms.


Those names won't help you. You want to identify (groups of) single
molecules. Look at your file and see what distinguishes them.

With gmx select I will enter the following command, at an arbitrarily
chosen time:
gmx select -f input.trr -s input.tpr -on output.ndx -b 7.5 -e 7.5
In the following selection screen my preferred molecules are listed as
three different groups (Eth, EthE and EthB), therefore I manually
select these groups with the command: resname Eth EthE EthB, press
enter and end with Ctrl-D. It will then proceed to process the frames,
where GROMACS tells me it has analyzed 1 frame, at the 30th timestep,
which is 7.5.


I can't see everything, but probably all you did was select every atom,
which won't help you. You wanted all the molecules with some criterion, so
you will need to make a better selection.

I will then switch to gmx traj where I enter the following:
gmx traj -f input.trr -s input.tpr -n output.ndx -ov output.xvg
It will then process all frames, and not only the frame I selected
during gmx select. Do I need to specify -b and -e again during gmx
traj?


Yes, once you've made a selection that matches geometric criteria from a
frame, it is literally only applicable to that frame.

Then, the output could be read with xmgrace, however looking at the
files it will try to plot 25000 different lines, which it probably
cant. Opening the .xvg file plots the velocity/time plot of only 1
atom, while opening the  .xvg file for the time selected output (via
gmx traj -b -e) shows an empty plot for only one atom.


You haven't selected eg one molecule from one frame yet, so get that right
first.

Mark

I'm getting lost in all the options, any help would be appreciated.

Mark
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Re: [gmx-users] Free energy calculations

[Mark Abraham]

Hi,

There's a very large literature on binding free energy calculations, and
most of the methods can be implemented in GROMACS.

Mark

On Thu, 2 Mar 2017 06:50 Amir Zeb  wrote:

> Hello gmx-users
>
> I wanted to compute binding free energy for a protein-ligand complex by
> gromacs. I sued MM/PBSA approach
>
> http://rashmikumari.github.io/g_mmpbsa/
>
> but here the entropic terms could not be computed which is the backbone
> limitation to restrict the actual free energy determination.
>
> Please let me know how may I calculate binding free energy in gromacs other
> than MM/PBSA approach?
>
> Thanks in advance!
>
> Amir
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Re: [gmx-users] Gromac4.6.7 installation problem

[Mark Abraham]

Hi,

Using parallel make obscures problems when they exist, so run again with
simple make. Probably cuda does not support your compiler, so you will run
into problems later. I suggest gcc 4.9

Mark

On Thu, 2 Mar 2017 06:58 Mohsen Ramezanpour 
wrote:

> Dear Gromacs users,
>
> I am trying to install gromacs 4.6.7 on Ubuntu 16.04.
> Unfortunately, I get an Error which I do not know how to solve it.
>
> After
> mkdir build
> cd build
>
> *I use:*
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_GPU=ON
> -DCMAKE_INSTALL_PREFIX=/home/mohsen/programs
> -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/5
> -L/usr/lib/gcc/x86_64-linux-gnu/5"
>
> *I get this:*
> -- The C compiler identification is GNU 5.4.0
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Looking for NVIDIA GPUs present in the system
> -- Number of NVIDIA GPUs detected: 1
> -- Looking for pthread.h
> -- Looking for pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - not found
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- Found CUDA: /usr (found suitable version "7.5", minimum required is
> "3.2")
> -- The CXX compiler identification is GNU 5.4.0
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Checking for GCC x86 inline asm
> -- Checking for GCC x86 inline asm - supported
> -- Detecting best acceleration for this CPU
> CMake Warning (dev) at cmake/gmxDetectAcceleration.cmake:65 (set):
>   Policy CMP0053 is not set: Simplify variable reference and escape
> sequence
>   evaluation.  Run "cmake --help-policy CMP0053" for policy details.  Use
> the
>   cmake_policy command to set the policy and suppress this warning.
>
>   For input:
>
> '@GCC_INLINE_ASM_DEFINE@ -I${CMAKE_SOURCE_DIR}/include
> -DGMX_CPUID_STANDALONE'
>
>   the old evaluation rules produce:
>
> '-DGMX_X86_GCC_INLINE_ASM
> -I/home/mohsen/Downloads/gromacs-4.6.7/include -DGMX_CPUID_STANDALONE'
>
>   but the new evaluation rules produce:
>
> '@GCC_INLINE_ASM_DEFINE@
> -I/home/mohsen/Downloads/gromacs-4.6.7/include
> -DGMX_CPUID_STANDALONE'
>
>   Using the old result for compatibility since the policy is not set.
> Call Stack (most recent call first):
>   cmake/gmxDetectAcceleration.cmake:98 (gmx_suggest_x86_acceleration)
>   CMakeLists.txt:184 (gmx_detect_acceleration)
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
> *and similar blocks like this again and again.*
>
>
> *it ends up with:*.
> .
> .
> -- [download 96% complete]
> -- [download 97% complete]
> -- [download 98% complete]
> -- [download 99% complete]
> -- [download 100% complete]
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/mohsen/Downloads/gromacs-4.6.7/build
>
>
>
>
>
> *So, I use:*
> *make -j 16*
>
> *and I get lots of lines which end with:*
>
> .
> .
> .
> Making install in neon
> Making install in reodft
> Making install in api
>  /usr/bin/install -c -m 644
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3.h
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3.f
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3l.f03
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3q.f03
>
> '/home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/include'
>  /usr/bin/install -c -m 644 fftw3.f03
>
> '/home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/include'
> Making install in libbench2
> Making install in .
>  /bin/bash ./libtool   --mode=install /usr/bin/install -c   libfftw3f.la
>
> '/home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/lib'
>  /usr/bin/install -c -m 644 fftw3f.pc
>
> '/home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'
> libtool: install: /usr/bin/install -c .libs/libfftw3f.lai
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/lib/
> libfftw3f.la
> libtool: install: /usr/bin/install -c .libs/libfftw3f.a
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a
> libtool: install: chmod 644
>
> /home/mohsen/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/

Re: [gmx-users] MM/Pbsa

[Mark Abraham]

Hi,

Looks like the tool is broken or you've not followed the instructions, or
they are not correct. I suggest starting again and being more careful this
time. Since this is not a gromacs tool, please discuss further with the
author.

Mark

On Thu, 2 Mar 2017 11:25 Kingsley Theras Primus Dass . <
105726...@gms.tcu.edu.tw> wrote:

> Hi,
>  I tried to calculate binding free energy for my protein. I tried using MM
> / PBSA, when i ran the program i am getting an error. Could you please say
> why such error is occuring and how should i need to rectify it.
>
>
>
> the error message is below
>
>
> 17:54:41
>  The directory RUN_ is not present. Please check the INPUT.dat file or run
> "gmxpbsa0.pbs".
> Exiting -
>
>
> Thank you.
>
> Kingsley Theras
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Re: [gmx-users] Catenation and sampling

[Mark Abraham]

Hi,

You can't concatenate trajectories and expect them to behave as if they
were continuous. Apparently three of your simulations show similar
behaviour and two different, perhaps explained by a transition in your
equilibration run after 2 ns.

In the limit of ergodic sampling, your protocol for five runs would be
fine, but by starting them all from similar systems, you build in a
starting similarity that you now have to correct for. That period of
similarity is hard to measure, but will be lower if you generate different
velocities before five separate equilibrations.

Mark

On Thu, 2 Mar 2017 17:40 suniba shuaib  wrote:

> Dear users and experts
>
> I have simulated a protein in water using OPLS-AA force field. Initially I
> performed a 5 ns simulation and then extracted frames out of it e.g. at
> 1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
> extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
> etc..). My question is how should I catenate these trajectories in order to
> ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
> RMSD and Rg which showed very high fluctuation till 150 ns and then was
> quiet stable till the end of 500ns. I am confused if these extra high
> fluctuations are due to poor sampling or improper catenation. Please help
> me.
>
> The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
> stayed between 1.0-1.1 nm.
>
> With Regards
> Suniba
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Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Mark Abraham]

Hi,

PDB has a well defined fixed-width field format:
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
so only columns 13-16 can contain the atom name. By eye, it looks like the
cgenff python script gets this wrong, using 14-17 (but do check in the
actual files). If so, please report that to them to get it fixed.

Fortunately, you can fix the file to move the space in column 13 to column
18 pretty easily, eg with the Unix cut and paste command line tools.

Mark

On Fri, 3 Mar 2017 05:28 Jonathan Saboury  wrote:

> I think I narrowed it down to the problem. This time I only simulated MIY
> in water and the problem occurs in gmx solvate and gmx grompp
>
> gmx solvate seems to only reads a max of 3 chars for atom type/number (not
> sure the correct name, it is the 3rd entry in pdb). This results in the
> output pdb invalid if the atom type/name has 3+ chars (4 in the case of the
> cgenff generated itps.
>
> Here is the comparison below:
> terminal IO: http://pastebin.com/raw/Vzibp4U0
> miy_b4_solv.pdb: http://pastebin.com/raw/CG8S3scz
> miy_b4_ion.pdb: http://pastebin.com/raw/1StxheeJ
>
> Fixing the atom types does not solve this problem however (grompp still
> only reading 3 chars?).
> So either gmx solvate/grompp  needs to fix their atom type reading or
> cgenff needs to fix their atom naming?
>
> Just wanted to confirm this is the correct assessment of the  problem with
> you before proceeding to ask for changes :)
>
> Thanks as always!
>
> - Jonathan
>
> On Thu, Mar 2, 2017 at 2:57 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 3/2/17 5:55 PM, Jonathan Saboury wrote:
> >
> >> Dear Justin
> >>
> >> Do you mean the "Include parameters that are already in CGenFF" option?
> I
> >> didn't tick that option but I did have to tick "guess bond orders from
> >> connectivity" or else it would error because of hypervalent carbon (5
> >> bonds)
> >>
> >>
> > Yeah, that's the box.  The only way I can think of to get overriding
> > parameters is to include things that are already present in the force
> field.
> >
> > -Justin
> >
> > Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg
> >>
> >> Thanks!
> >>
> >> - Jonathan
> >> 
> >>
> >>
> >>
> >>
> >> On Thu, Mar 2, 2017 at 2:07 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 3/2/17 3:17 PM, Jonathan Saboury wrote:
> >>>
> >>> Hello all,
> 
>  I'm trying to run a simulation of 2DRD in water with
> charmm36-nov2016.ff
>  (AcrB co complexed with minocycline). The main problem I'm having is
>  generating an .itp of minocycline (getting it from a reference would
> not
>  work for me as I need to simulate other small organic molecules not in
>  literature). I have run md on 2drd not complexed successfully with the
>  same
>  methodology.
> 
>  I've tried charmm-gui and that worked but that was messy as I needed
> to
>  include two forcefields:
>  ./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded
>  to
>  overriding Bond parameters. What parameters were overridden and the
>  effect
>  of that I have no idea (hopefully you can enlighten me).
> 
> 
>  If you are building a system with CHARMM-GUI, you should not make any
> >>> changes whatsoever to the topology it gives you.  The reason is that
> what
> >>> CHARMM-GUI does is extract only the necessary subset of the CHARMM
> force
> >>> field that is relevant to your system and put it in an all-included
> >>> topology.  This is different from the "normal" GROMACS approach of
> >>> constructing a whole force field and then using a subset of it.
> >>>
> >>> So I tried CGenFF. This generated the itp (along with a prm) with the
> ff
> >>> I
> >>>
>  wanted was used, no other ff was included (yay!).
> 
>  However, this led to a "overriding Bond parameters" as well as a
> number
>  of
>  coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not
>  match
>  topology (topol.top, 434665) error. I'm fairly sure my .top file
>  includes
>  everything correctly, so I'm thinking that somehow this .prm/.itp
> messed
>  up
>  with original ff and added some atoms. Or did I do something very
>  stupid?
> 
>  Terminal IO: http://pastebin.com/raw/KY6SRtdm
>  topol.top: http://pastebin.com/raw/fKJfpr6a
>  Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar
> 
> 
>  The errors suggest you enabled the option to include all relevant
> force
> >>> field parameters in the resulting stream file.  This will cause overlap
> >>> with the existing force field, which is not what you want.
> >>>
> >>> -Justin
> >>>
> >>> Thank you for the help, I really appreciate it :-)
> >>>
> 
>  - Jonathan
> 
> 
>  --
> >>> ==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmace

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Amir Zeb]

Hi Dr. Justin,

I'm wondering that you have mentioned CHARMm27 is not a valid identifier of
protein forcefield, but we have so many articles already published while
using CHARMm27 ff. Can you please let us know how to trace this
unsuitability of CHARMm27 especially for protein-ligand simulation?

Thanks

-Amir

On Thu, Mar 2, 2017 at 2:10 PM, Justin Lemkul  wrote:

>
>
> On 3/2/17 2:16 PM, Sanim Rahman wrote:
>
>> Hi all,
>>
>> I am attempting to run a membrane protein simulation where I am describing
>> my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36.
>> When
>> I use the grompp command, I get the following error:
>>
>> Fatal error:
>> Syntax error - File forcefield.itp, line 9
>> Last line read:
>> '[ defaults ]'
>> Invalid order for directive defaults
>>
>> To create my topology file, I took my protein.top and at the bottom
>> included my lipid.itp and solvent.itp. The error is referencing to my
>> charmm36 force field file. I was unsure what to do so I just removed the
>> line with [ defaults ] on it and tried running it again. This time I
>> received this error:
>>
>> Fatal error:
>> Syntax error - File ffnonbonded.itp, line 5
>> Last line read:
>> '[ atomtypes ]'
>> Invalid order for directive atomtypes
>>
>> Is the source of the error from how my topology files are processing the
>> force field files since I am using both CHARMM27 and CHARMM36? I read a
>> previous thread that you can't have two [ default ] lines which make sense
>> but I am unsure of what is the proper protocol to get around this to
>> include both force fields. Any help will be deeply appreciated!
>>
>>
> I mentioned this last week in another thread, but I'll say it again:
> "CHARMM27" is not a valid identifier for a protein force field.  What
> you're trying to use is CHARMM22/CMAP.
>
> The bigger question is why you want to use this combination?  It may not
> be practical or possible to do so in GROMACS.  You'll likely have to hack
> out the bonded and nonbonded parameters that relate to proteins and marry
> them together with the lipid-only portions of CHARMM36.
>
> -Justin
>
> Thank You,
>>
>> *Sanim Rahman*
>> B.S. Chemical Engineering, 2019
>> Resident Assistant, Castor Hall Engineering Living Learning Community
>> 2016-2017
>> Co-Founder and Co-President of the Undergraduate Research Society
>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Per lipid area for heterogeneous membrane

[Мижээ Батсайхан]

Dear Justin,
Thank you very much.

I analyzed 1001 frames of trajectory. All outputs are written in separate
files. How can I summarize over all time?

Best regards,
Mijee

>
> On 3/2/17 12:34 AM, ? ? wrote:
> > Dear Justin,
> >
> > Thank you very much for your reply. I have a further question about
> > GridMAT-MD tool. Is it possible to use in case with different upper
> leaflet
> > and lower leaflet? In the manual, GridMAT-MD tool needs the leaflet tails
> > face towards.
> >
>
> We split the membrane based on the "middle" of the lipid coordinates, so
> "top"
> and "bottom" may be inverted if your membrane is, e.g. split across PBC.
> But
> those designators are arbitrary anyway in a periodic system, so you just
> have to
> keep track of what is what.
>
> -Justin
>
> > Best regards,
> > Mijee
> >
> > On 3/1/17 8:56 AM, ? ? wrote:
> >>> Dear gmx users,
> >>>
> >>> Hello, My simulation system consists of severil different type of
> >> membrane
> >>> models including ergosterols. I want to analysis per lipid area for
> this
> >>> system. How can I calculate the area? Please advice me.
> >>>
> >>> Can I use GridMAT-MD tool? If it is possible, how I do.
> >>>
> >>
> >> Yes, and we provide an example of a mixed bilayer in section 7.2 of our
> >> PDF manual.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
>
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Jonathan Saboury]

I think I narrowed it down to the problem. This time I only simulated MIY
in water and the problem occurs in gmx solvate and gmx grompp

gmx solvate seems to only reads a max of 3 chars for atom type/number (not
sure the correct name, it is the 3rd entry in pdb). This results in the
output pdb invalid if the atom type/name has 3+ chars (4 in the case of the
cgenff generated itps.

Here is the comparison below:
terminal IO: http://pastebin.com/raw/Vzibp4U0
miy_b4_solv.pdb: http://pastebin.com/raw/CG8S3scz
miy_b4_ion.pdb: http://pastebin.com/raw/1StxheeJ

Fixing the atom types does not solve this problem however (grompp still
only reading 3 chars?).
So either gmx solvate/grompp  needs to fix their atom type reading or
cgenff needs to fix their atom naming?

Just wanted to confirm this is the correct assessment of the  problem with
you before proceeding to ask for changes :)

Thanks as always!

- Jonathan

On Thu, Mar 2, 2017 at 2:57 PM, Justin Lemkul  wrote:

>
>
> On 3/2/17 5:55 PM, Jonathan Saboury wrote:
>
>> Dear Justin
>>
>> Do you mean the "Include parameters that are already in CGenFF" option? I
>> didn't tick that option but I did have to tick "guess bond orders from
>> connectivity" or else it would error because of hypervalent carbon (5
>> bonds)
>>
>>
> Yeah, that's the box.  The only way I can think of to get overriding
> parameters is to include things that are already present in the force field.
>
> -Justin
>
> Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg
>>
>> Thanks!
>>
>> - Jonathan
>> 
>>
>>
>>
>>
>> On Thu, Mar 2, 2017 at 2:07 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 3/2/17 3:17 PM, Jonathan Saboury wrote:
>>>
>>> Hello all,

 I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
 (AcrB co complexed with minocycline). The main problem I'm having is
 generating an .itp of minocycline (getting it from a reference would not
 work for me as I need to simulate other small organic molecules not in
 literature). I have run md on 2drd not complexed successfully with the
 same
 methodology.

 I've tried charmm-gui and that worked but that was messy as I needed to
 include two forcefields:
 ./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded
 to
 overriding Bond parameters. What parameters were overridden and the
 effect
 of that I have no idea (hopefully you can enlighten me).


 If you are building a system with CHARMM-GUI, you should not make any
>>> changes whatsoever to the topology it gives you.  The reason is that what
>>> CHARMM-GUI does is extract only the necessary subset of the CHARMM force
>>> field that is relevant to your system and put it in an all-included
>>> topology.  This is different from the "normal" GROMACS approach of
>>> constructing a whole force field and then using a subset of it.
>>>
>>> So I tried CGenFF. This generated the itp (along with a prm) with the ff
>>> I
>>>
 wanted was used, no other ff was included (yay!).

 However, this led to a "overriding Bond parameters" as well as a number
 of
 coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not
 match
 topology (topol.top, 434665) error. I'm fairly sure my .top file
 includes
 everything correctly, so I'm thinking that somehow this .prm/.itp messed
 up
 with original ff and added some atoms. Or did I do something very
 stupid?

 Terminal IO: http://pastebin.com/raw/KY6SRtdm
 topol.top: http://pastebin.com/raw/fKJfpr6a
 Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar


 The errors suggest you enabled the option to include all relevant force
>>> field parameters in the resulting stream file.  This will cause overlap
>>> with the existing force field, which is not what you want.
>>>
>>> -Justin
>>>
>>> Thank you for the help, I really appreciate it :-)
>>>

 - Jonathan


 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 

Re: [gmx-users] Per lipid area for heterogeneous membrane

[Мижээ Батсайхан]

Dear Bjorn,

Thank you very much for sending APL software information. I will ask you if
there is a problem.

Best regards,
Mijee

--
>
> Message: 4
> Date: Thu, 2 Mar 2017 10:05:31 +0100
> From: Bj?rn Sommer 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Per lipid area for heterogeneous membrane
>
> Dear Mijee,
>
> alternatively to GridMat, you might also want to have a look at our
> APL@Voro:
>
> http://aplvoro.org
>
> It provides a GUI, so you can easily import your PDB file into the tool
> and analyze the APL, thickness and neighborhood based on Voronoi
> tesselation. Later, you can also import trajectory files and analyze
> them over time. The publication reference you will also find at the
> website.
>
> Cheers,
> Bjorn
>
-- 
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Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Justin Lemkul]

On 3/2/17 5:55 PM, Jonathan Saboury wrote:

Dear Justin

Do you mean the "Include parameters that are already in CGenFF" option? I
didn't tick that option but I did have to tick "guess bond orders from
connectivity" or else it would error because of hypervalent carbon (5
bonds)



Yeah, that's the box.  The only way I can think of to get overriding parameters 
is to include things that are already present in the force field.


-Justin


Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg

Thanks!

- Jonathan




On Thu, Mar 2, 2017 at 2:07 PM, Justin Lemkul  wrote:




On 3/2/17 3:17 PM, Jonathan Saboury wrote:


Hello all,

I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
(AcrB co complexed with minocycline). The main problem I'm having is
generating an .itp of minocycline (getting it from a reference would not
work for me as I need to simulate other small organic molecules not in
literature). I have run md on 2drd not complexed successfully with the
same
methodology.

I've tried charmm-gui and that worked but that was messy as I needed to
include two forcefields:
./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded to
overriding Bond parameters. What parameters were overridden and the effect
of that I have no idea (hopefully you can enlighten me).



If you are building a system with CHARMM-GUI, you should not make any
changes whatsoever to the topology it gives you.  The reason is that what
CHARMM-GUI does is extract only the necessary subset of the CHARMM force
field that is relevant to your system and put it in an all-included
topology.  This is different from the "normal" GROMACS approach of
constructing a whole force field and then using a subset of it.

So I tried CGenFF. This generated the itp (along with a prm) with the ff I

wanted was used, no other ff was included (yay!).

However, this led to a "overriding Bond parameters" as well as a number of
coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not match
topology (topol.top, 434665) error. I'm fairly sure my .top file includes
everything correctly, so I'm thinking that somehow this .prm/.itp messed
up
with original ff and added some atoms. Or did I do something very stupid?

Terminal IO: http://pastebin.com/raw/KY6SRtdm
topol.top: http://pastebin.com/raw/fKJfpr6a
Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar



The errors suggest you enabled the option to include all relevant force
field parameters in the resulting stream file.  This will cause overlap
with the existing force field, which is not what you want.

-Justin

Thank you for the help, I really appreciate it :-)


- Jonathan



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Jonathan Saboury]

Dear Justin

Do you mean the "Include parameters that are already in CGenFF" option? I
didn't tick that option but I did have to tick "guess bond orders from
connectivity" or else it would error because of hypervalent carbon (5
bonds)

Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg

Thanks!

- Jonathan




On Thu, Mar 2, 2017 at 2:07 PM, Justin Lemkul  wrote:

>
>
> On 3/2/17 3:17 PM, Jonathan Saboury wrote:
>
>> Hello all,
>>
>> I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
>> (AcrB co complexed with minocycline). The main problem I'm having is
>> generating an .itp of minocycline (getting it from a reference would not
>> work for me as I need to simulate other small organic molecules not in
>> literature). I have run md on 2drd not complexed successfully with the
>> same
>> methodology.
>>
>> I've tried charmm-gui and that worked but that was messy as I needed to
>> include two forcefields:
>> ./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded to
>> overriding Bond parameters. What parameters were overridden and the effect
>> of that I have no idea (hopefully you can enlighten me).
>>
>>
> If you are building a system with CHARMM-GUI, you should not make any
> changes whatsoever to the topology it gives you.  The reason is that what
> CHARMM-GUI does is extract only the necessary subset of the CHARMM force
> field that is relevant to your system and put it in an all-included
> topology.  This is different from the "normal" GROMACS approach of
> constructing a whole force field and then using a subset of it.
>
> So I tried CGenFF. This generated the itp (along with a prm) with the ff I
>> wanted was used, no other ff was included (yay!).
>>
>> However, this led to a "overriding Bond parameters" as well as a number of
>> coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not match
>> topology (topol.top, 434665) error. I'm fairly sure my .top file includes
>> everything correctly, so I'm thinking that somehow this .prm/.itp messed
>> up
>> with original ff and added some atoms. Or did I do something very stupid?
>>
>> Terminal IO: http://pastebin.com/raw/KY6SRtdm
>> topol.top: http://pastebin.com/raw/fKJfpr6a
>> Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar
>>
>>
> The errors suggest you enabled the option to include all relevant force
> field parameters in the resulting stream file.  This will cause overlap
> with the existing force field, which is not what you want.
>
> -Justin
>
> Thank you for the help, I really appreciate it :-)
>>
>> - Jonathan
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Distance between centers of mass

[Justin Lemkul]

On 3/2/17 4:15 PM, ÁLVARO RODRIGO RUIZ FERNÁNDEZ wrote:

Dear GROMACS users:

How can I calculate the distance between centers of mass of two residues in
time with gmx distance?, I do not understand the  sentence "com of resname
AAA plus com of resname BBB"  from the manual, pag 241 . Thanks.




This is simply the selection syntax for doing exactly what you describe.  You 
can select by residue name, number, etc. or by an existing index group, e.g.


gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'"

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Justin Lemkul]

On 3/2/17 2:16 PM, Sanim Rahman wrote:

Hi all,

I am attempting to run a membrane protein simulation where I am describing
my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36. When
I use the grompp command, I get the following error:

Fatal error:
Syntax error - File forcefield.itp, line 9
Last line read:
'[ defaults ]'
Invalid order for directive defaults

To create my topology file, I took my protein.top and at the bottom
included my lipid.itp and solvent.itp. The error is referencing to my
charmm36 force field file. I was unsure what to do so I just removed the
line with [ defaults ] on it and tried running it again. This time I
received this error:

Fatal error:
Syntax error - File ffnonbonded.itp, line 5
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

Is the source of the error from how my topology files are processing the
force field files since I am using both CHARMM27 and CHARMM36? I read a
previous thread that you can't have two [ default ] lines which make sense
but I am unsure of what is the proper protocol to get around this to
include both force fields. Any help will be deeply appreciated!



I mentioned this last week in another thread, but I'll say it again: "CHARMM27" 
is not a valid identifier for a protein force field.  What you're trying to use 
is CHARMM22/CMAP.


The bigger question is why you want to use this combination?  It may not be 
practical or possible to do so in GROMACS.  You'll likely have to hack out the 
bonded and nonbonded parameters that relate to proteins and marry them together 
with the lipid-only portions of CHARMM36.


-Justin


Thank You,

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Catenation and sampling

[Justin Lemkul]

On 3/2/17 11:40 AM, suniba shuaib wrote:

Dear users and experts

I have simulated a protein in water using OPLS-AA force field. Initially I
performed a 5 ns simulation and then extracted frames out of it e.g. at
1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
etc..). My question is how should I catenate these trajectories in order to
ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
RMSD and Rg which showed very high fluctuation till 150 ns and then was
quiet stable till the end of 500ns. I am confused if these extra high
fluctuations are due to poor sampling or improper catenation. Please help
me.



You can easily resolve this by analyzing each trajectory separately (probably 
more appropriate in this case for such simple analysis) and also visualizing the 
trajectories.  If you've got one or more systems that are behaving differently, 
your best tool isn't written in code, it's your eyes :)


-Justin


The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
stayed between 1.0-1.1 nm.

With Regards
Suniba



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Justin Lemkul]

On 3/2/17 3:17 PM, Jonathan Saboury wrote:

Hello all,

I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
(AcrB co complexed with minocycline). The main problem I'm having is
generating an .itp of minocycline (getting it from a reference would not
work for me as I need to simulate other small organic molecules not in
literature). I have run md on 2drd not complexed successfully with the same
methodology.

I've tried charmm-gui and that worked but that was messy as I needed to
include two forcefields:
./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded to
overriding Bond parameters. What parameters were overridden and the effect
of that I have no idea (hopefully you can enlighten me).



If you are building a system with CHARMM-GUI, you should not make any changes 
whatsoever to the topology it gives you.  The reason is that what CHARMM-GUI 
does is extract only the necessary subset of the CHARMM force field that is 
relevant to your system and put it in an all-included topology.  This is 
different from the "normal" GROMACS approach of constructing a whole force field 
and then using a subset of it.



So I tried CGenFF. This generated the itp (along with a prm) with the ff I
wanted was used, no other ff was included (yay!).

However, this led to a "overriding Bond parameters" as well as a number of
coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not match
topology (topol.top, 434665) error. I'm fairly sure my .top file includes
everything correctly, so I'm thinking that somehow this .prm/.itp messed up
with original ff and added some atoms. Or did I do something very stupid?

Terminal IO: http://pastebin.com/raw/KY6SRtdm
topol.top: http://pastebin.com/raw/fKJfpr6a
Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar



The errors suggest you enabled the option to include all relevant force field 
parameters in the resulting stream file.  This will cause overlap with the 
existing force field, which is not what you want.


-Justin


Thank you for the help, I really appreciate it :-)

- Jonathan



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] linking error while trying to build gromacs

[Andrey Tolstov]

Hello! I'm trying to install gromacs 5.1.4 on my Ubuntu 16.04. I've unpacked sources, made build dir, launched from it "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DGMX_DOUBLE=off" - it worked fine, then ran "make". Compilation was ok, but linker returned an error "collect2: error: ld returned 1 exit status" and a lot of undefined references, like that: [ 98%] Linking CXX executable ../../bin/template../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_avx_256_single'../../lib/libgromacs.so.1.4.0: undefined reference to `nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn'../../lib/libgromacs.so.1.4.0: undefined reference to `nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single' After that I've tried to build and use fftw3, switch from avx to sse4.1, switch from gcc-5 to gcc-4.9, but these (or very similar) errors didn't disappear. Also I've tried gromacs versions 5.1.3 and 5.0.4 but I've got the same problem.For more information see the full make log by link http://pastebin.com/UeyfPdgA or tail of it with all the errors in attached file.Can you please help me finding the reason of this problem? Thanks in advance,Andrey[ 97%] Building C object 
src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
[ 97%] Linking CXX shared library ../../lib/libgromacs.so
[ 97%] Built target libgromacs
Scanning dependencies of target template
[ 97%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
[ 97%] Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_avx_256_single'
../../lib/libgromacs.so.1.4.0: undefined reference to 
`nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_avx_256_single'
../.

[gmx-users] Distance between centers of mass

[ÁLVARO RODRIGO RUIZ FERNÁNDEZ]

Dear GROMACS users:

How can I calculate the distance between centers of mass of two residues in
time with gmx distance?, I do not understand the  sentence "com of resname
AAA plus com of resname BBB"  from the manual, pag 241 . Thanks.


-- 

*Dr. Álvaro  Ruiz  *



*Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de
CienciasUniversidad de Chile*Mobile: +56-9-51178101
Office: +56-2-9787443
arr...@ug.uchile.cl
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[gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

[Jonathan Saboury]

Hello all,

I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
(AcrB co complexed with minocycline). The main problem I'm having is
generating an .itp of minocycline (getting it from a reference would not
work for me as I need to simulate other small organic molecules not in
literature). I have run md on 2drd not complexed successfully with the same
methodology.

I've tried charmm-gui and that worked but that was messy as I needed to
include two forcefields:
./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded to
overriding Bond parameters. What parameters were overridden and the effect
of that I have no idea (hopefully you can enlighten me).

So I tried CGenFF. This generated the itp (along with a prm) with the ff I
wanted was used, no other ff was included (yay!).

However, this led to a "overriding Bond parameters" as well as a number of
coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not match
topology (topol.top, 434665) error. I'm fairly sure my .top file includes
everything correctly, so I'm thinking that somehow this .prm/.itp messed up
with original ff and added some atoms. Or did I do something very stupid?

Terminal IO: http://pastebin.com/raw/KY6SRtdm
topol.top: http://pastebin.com/raw/fKJfpr6a
Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar

Thank you for the help, I really appreciate it :-)

- Jonathan
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Re: [gmx-users] Updating/upgrading GROMACS

[Szilárd Páll]

Hi Gregory,

If you have installed in the default system location, you definitely
should clean up before you install a new version (if you did not
change the default path, you can just remove /usr/local/gromacs).

However, you can keep multiple installations and simply use whichever
you need? All you need to do is pass e.g.
-D CMAKE_INSTALL_PREFIX=/somepath/gromacs-2016.2
to the cmake invocation and before using the new installation do
source /somepath/gromacs-2016.2/bin/GMXRC

This way you can easily switch between versions, compare, or keep
working concurrently on different projects with the same version that
you started out with!

Cheers,
--
Szilárd


On Thu, Mar 2, 2017 at 6:02 PM, Gregory Poon  wrote:
> Hello all:
>
> I would like to get some advice on updating/upgrading an existing GROMACS
> installation.  I realize that this may actually be a more general
> UNIX/ubuntu question, but I really would like to not foul this up on the
> local machines that we really need to keep running. In particular, could I
> do something as naive-sounding as renaming the existing folder in
> /usr/local/ and proceeding with a new installation?  Would linking to the
> GPU library complicate matters?
>
> If it matters, we have machines that are running 5.1.4 and 2016.1 that I
> would like to have 2016.2 running.
>
> Many thanks in advance,
> Gregory
> --
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[gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Sanim Rahman]

Hi all,

I am attempting to run a membrane protein simulation where I am describing
my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36. When
I use the grompp command, I get the following error:

Fatal error:
Syntax error - File forcefield.itp, line 9
Last line read:
'[ defaults ]'
Invalid order for directive defaults

To create my topology file, I took my protein.top and at the bottom
included my lipid.itp and solvent.itp. The error is referencing to my
charmm36 force field file. I was unsure what to do so I just removed the
line with [ defaults ] on it and tried running it again. This time I
received this error:

Fatal error:
Syntax error - File ffnonbonded.itp, line 5
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

Is the source of the error from how my topology files are processing the
force field files since I am using both CHARMM27 and CHARMM36? I read a
previous thread that you can't have two [ default ] lines which make sense
but I am unsure of what is the proper protocol to get around this to
include both force fields. Any help will be deeply appreciated!

Thank You,

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research
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[gmx-users] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa

[Atila Petrosian]

Dear Amber users,

I did mm-gbsa calculation for my protein-ligand complex.

Differences (Complex - Receptor - Ligand):
Energy ComponentAverage  Std. Dev.   Std. Err. of
Mean
---
BOND 0.0.0001
 0.
ANGLE   -0.0.
 0.
DIHED   -0.0.0001
 0.
VDWAALS-38.38053.4143
 0.2408
EEL-17.46586.7954
 0.4793
1-4 VDW  -2091.2911  525.5238
37.0676
1-4 EEL 25.34590.6995
 0.0493
EGB 39.24947.4730
 0.5271
ESURF   -5.21130.4671
 0.0329

DELTA G gas  -2121.7915  525.8067
37.0875
DELTA G solv34.03817.2074
 0.5084

DELTA TOTAL  -2087.7534  525.4087
37.0595


Are 1-4 VDW and 1-4 EEL Energy Components important?

1-4 VDW term is very large.

What is the definition of them?

Best,
Atila
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[gmx-users] Updating/upgrading GROMACS

[Gregory Poon]

Hello all:

I would like to get some advice on updating/upgrading an existing 
GROMACS installation.  I realize that this may actually be a more 
general UNIX/ubuntu question, but I really would like to not foul this 
up on the local machines that we really need to keep running. In 
particular, could I do something as naive-sounding as renaming the 
existing folder in /usr/local/ and proceeding with a new installation?  
Would linking to the GPU library complicate matters?


If it matters, we have machines that are running 5.1.4 and 2016.1 that I 
would like to have 2016.2 running.


Many thanks in advance,
Gregory
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[gmx-users] Catenation and sampling

[suniba shuaib]

Dear users and experts

I have simulated a protein in water using OPLS-AA force field. Initially I
performed a 5 ns simulation and then extracted frames out of it e.g. at
1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
etc..). My question is how should I catenate these trajectories in order to
ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
RMSD and Rg which showed very high fluctuation till 150 ns and then was
quiet stable till the end of 500ns. I am confused if these extra high
fluctuations are due to poor sampling or improper catenation. Please help
me.

The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
stayed between 1.0-1.1 nm.

With Regards
Suniba
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Re: [gmx-users] Gromacs with Plumed

[Szilárd Páll]

Hi,

I'd recommend keeping a vanilla/untainted GROMACS installation
available to users at all times. No matter how much awareness there is
about issues or unwanted code interaction, as long as a user is not
running an official GROMACS release, they can and should not claim
(e.g. in a publication) that they used "GROMACS vX.Y". This is not
just nitpicking, but a matter of scientific reproducibility.

I hope that PLUMED patching also changes the version string not just
the code so installations from "patched" source do not claim to be
vanilla, official GROMACS. Can you or someone else aware confirm that?


On a side-note, the uncomfortable side-effect of the patch-based
software distribution model would of course be easy to solve if thin
API abstractions were designed and submitted upstream in the main
GROMACS source.

Cheers,
--
Szilárd


On Thu, Mar 2, 2017 at 9:09 AM, Åke Sandgren  wrote:
> Hi!
>
> Are there any known drawbacks to building Gromacs with Plumed?
>
> I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
> both if there are problems with any version combination i'd like to know
> that too.
>
> I.e., will it cause problems for non-plumed runs, will gromacs behave
> identical to a non-plumed build when not using plumed in the
> plumed-build, etc.?
>
> Having just a single build makes my life easier :-)
>
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

[Acqualine Lobo]

Thank you so much! It worked! Really appreciate the quick reply.

Acqualine Lobo
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Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

[Justin Lemkul]

On 3/2/17 9:18 AM, Acqualine Lobo wrote:

Thanks for the quick reply Dr. Justin!

I did follow what you mentioned, however I still get the same error. I also
tried changing the residue name in the pdb file to match the atom type as
in the .atp file, the error still remains only with a different residue
name. Instead of "Residue 'CMO' not found in topology database" it says
"Residue 'CM' not found in topology database".

This is my first time using gromacs and I feel really lost. Any suggestions
are welcome.



There is nothing in the .atp file that will help you correct the .pdb file. 
Coordinate files have no type information, only residue and atom names.


The CHARMM36 residue is called "CO" (see the .rtp file, which is what matters) 
and the atoms are named simply C and O.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

[Acqualine Lobo]

Thanks for the quick reply Dr. Justin!

I did follow what you mentioned, however I still get the same error. I also
tried changing the residue name in the pdb file to match the atom type as
in the .atp file, the error still remains only with a different residue
name. Instead of "Residue 'CMO' not found in topology database" it says
"Residue 'CM' not found in topology database".

This is my first time using gromacs and I feel really lost. Any suggestions
are welcome.

Thanks in advance

Acqualine Lobo
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Re: [gmx-users] topology

[RAHUL SURESH]

i am getting an error. You have to set a -conect option
what is t?

On Thu, Mar 2, 2017 at 6:56 PM, Jakub Krajniak <
jakub.krajn...@cs.kuleuven.be> wrote:

> Did you try mktop ? (http://www.aribeiro.net.br/mktop)
>
>
>
> On 02.03.2017 05:23, RAHUL SURESH wrote:
>
>> Dear Justin
>>
>> Is there anything I can do to make this job easier?
>>
>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:
>>
>>
>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>>>
>>> Dear Justin

 What is the error here?
 I don't understand it.
 Can you be little more precise?


 The long and short of it TopolGen is very crudely coded and atom order
>>> matters because the script makes a lot of assumptions.  Your input PDB
>>> file
>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
>>> out what any of the actual functional groups are, so you get basically
>>> default atom types for everything.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:
>>>

 On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>
> This is my itp file(only a part)
>
>> I have highlighted two errors.. there are 19 such errors.
>> If I can know the reason for the error exactly it would be of a great
>> help
>> to me.
>>
>>
>> TopolGen relies on atom ordering to guess what the proper parameters
>>
> should be. It's pretty limited in what it can do.  A coordinate file
> that
> simply groups atoms by element is going to produce a totally garbage
> topology, unfortunately.
>
> -Justin
>
>
> [ atoms ]
>
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>> typeBchargeB  massB
>>   1   opls_154  1UNK  O  0 -0.580921
>> 15.99940
>>   2   opls_154  1UNK  O  0 -0.635654
>> 15.99940
>>   3   opls_516  1UNK  C  1 -0.112257
>> 12.01100
>>   4   opls_516  1UNK  C  2 -0.163224
>> 12.01100
>>   5   opls_516  1UNK  C  3  0.228741
>> 12.01100
>>   6   opls_516  1UNK  C  4 -0.304756
>> 12.01100
>>   7   opls_516  1UNK  C  5 -0.312217
>> 12.01100
>>   8   opls_145  1UNK  C  6  0.120569
>> 12.01100
>>   9   opls_145  1UNK  C  7  0.151897
>> 12.01100
>>  10   opls_145  1UNK  C  8  0.231044
>> 12.01100
>>  11   opls_516  1UNK  C  9 -0.401751
>> 12.01100
>>  12   opls_516  1UNK  C 10 -0.403094
>> 12.01100
>>  13   opls_145  1UNK  C 11 -0.150352
>> 12.01100
>>  14   opls_145  1UNK  C 12  0.193129
>> 12.01100
>>  15   opls_145  1UNK  C 13 -0.161115
>> 12.01100
>>  16   opls_516  1UNK  C 14 -0.471874
>> 12.01100
>>  17   opls_145  1UNK  C 15  0.100725
>> 12.01100
>>  18   opls_145  1UNK  C 16 -0.153943
>> 12.01100
>>  19   opls_516  1UNK  C 17 -0.330577
>> 12.01100
>>  20   opls_516  1UNK  C 18 -0.229875
>> 12.01100
>>  21   opls_135  1UNK  C 19 -0.229884
>> 12.01100
>>  22   opls_135  1UNK  C 20 -0.237230
>> 12.01100
>>  23   opls_135  1UNK  C 21 -0.404861
>> 12.01100
>>  24   opls_140  1UNK  H 21  0.135257
>> 1.00800
>>  25   opls_140  1UNK  H 21  0.154010
>> 1.00800
>>  26   opls_140  1UNK 2H 21  0.142643
>> 1.00800
>>  27   opls_140  1UNK 1H 21  0.133623
>> 1.00800
>>  28   opls_140  1UNK 2H 21  0.137323
>> 1.00800
>>  29   opls_140  1UNK 1H 21  0.167475
>> 1.00800
>>  30   opls_140  1UNK 1H 21  0.135348
>> 1.00800
>>  31   opls_140  1UNK 2H 21  0.153851
>> 1.00800
>>  32   opls_140  1UNK 3H 21  0.138487
>> 1.00800
>>  33   opls_140  1UNK 1H 21  0.137087
>> 1.00800
>>  34   opls_140  1UNK 2H 21  0.146500
>> 1.00800
>>  35   opls_140  1UNK 3H 21  0.148972
>> 1.00800
>>  36   opls_140  1UNK  H 21  0.103605
>> 1.00800
>>  37   opls_140  1UNK  H 21  0.127061
>> 1.00800
>>  38   opls_140  1UNK 1H 21  0.143100
>> 1.00800
>>  39   opls_140  1UNK 2H 21  0.137525
>> 1.00800
>

Re: [gmx-users] topology

[RAHUL SURESH]

Nope.. I havent tried that one.

If I am manually parametrizing a topology, then i shud add them in
aminoacids .rtp file? Should I make any change to gro file?

On Thu, Mar 2, 2017 at 6:56 PM, Jakub Krajniak <
jakub.krajn...@cs.kuleuven.be> wrote:

> Did you try mktop ? (http://www.aribeiro.net.br/mktop)
>
>
>
> On 02.03.2017 05:23, RAHUL SURESH wrote:
>
>> Dear Justin
>>
>> Is there anything I can do to make this job easier?
>>
>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:
>>
>>
>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>>>
>>> Dear Justin

 What is the error here?
 I don't understand it.
 Can you be little more precise?


 The long and short of it TopolGen is very crudely coded and atom order
>>> matters because the script makes a lot of assumptions.  Your input PDB
>>> file
>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
>>> out what any of the actual functional groups are, so you get basically
>>> default atom types for everything.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:
>>>

 On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>
> This is my itp file(only a part)
>
>> I have highlighted two errors.. there are 19 such errors.
>> If I can know the reason for the error exactly it would be of a great
>> help
>> to me.
>>
>>
>> TopolGen relies on atom ordering to guess what the proper parameters
>>
> should be. It's pretty limited in what it can do.  A coordinate file
> that
> simply groups atoms by element is going to produce a totally garbage
> topology, unfortunately.
>
> -Justin
>
>
> [ atoms ]
>
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>> typeBchargeB  massB
>>   1   opls_154  1UNK  O  0 -0.580921
>> 15.99940
>>   2   opls_154  1UNK  O  0 -0.635654
>> 15.99940
>>   3   opls_516  1UNK  C  1 -0.112257
>> 12.01100
>>   4   opls_516  1UNK  C  2 -0.163224
>> 12.01100
>>   5   opls_516  1UNK  C  3  0.228741
>> 12.01100
>>   6   opls_516  1UNK  C  4 -0.304756
>> 12.01100
>>   7   opls_516  1UNK  C  5 -0.312217
>> 12.01100
>>   8   opls_145  1UNK  C  6  0.120569
>> 12.01100
>>   9   opls_145  1UNK  C  7  0.151897
>> 12.01100
>>  10   opls_145  1UNK  C  8  0.231044
>> 12.01100
>>  11   opls_516  1UNK  C  9 -0.401751
>> 12.01100
>>  12   opls_516  1UNK  C 10 -0.403094
>> 12.01100
>>  13   opls_145  1UNK  C 11 -0.150352
>> 12.01100
>>  14   opls_145  1UNK  C 12  0.193129
>> 12.01100
>>  15   opls_145  1UNK  C 13 -0.161115
>> 12.01100
>>  16   opls_516  1UNK  C 14 -0.471874
>> 12.01100
>>  17   opls_145  1UNK  C 15  0.100725
>> 12.01100
>>  18   opls_145  1UNK  C 16 -0.153943
>> 12.01100
>>  19   opls_516  1UNK  C 17 -0.330577
>> 12.01100
>>  20   opls_516  1UNK  C 18 -0.229875
>> 12.01100
>>  21   opls_135  1UNK  C 19 -0.229884
>> 12.01100
>>  22   opls_135  1UNK  C 20 -0.237230
>> 12.01100
>>  23   opls_135  1UNK  C 21 -0.404861
>> 12.01100
>>  24   opls_140  1UNK  H 21  0.135257
>> 1.00800
>>  25   opls_140  1UNK  H 21  0.154010
>> 1.00800
>>  26   opls_140  1UNK 2H 21  0.142643
>> 1.00800
>>  27   opls_140  1UNK 1H 21  0.133623
>> 1.00800
>>  28   opls_140  1UNK 2H 21  0.137323
>> 1.00800
>>  29   opls_140  1UNK 1H 21  0.167475
>> 1.00800
>>  30   opls_140  1UNK 1H 21  0.135348
>> 1.00800
>>  31   opls_140  1UNK 2H 21  0.153851
>> 1.00800
>>  32   opls_140  1UNK 3H 21  0.138487
>> 1.00800
>>  33   opls_140  1UNK 1H 21  0.137087
>> 1.00800
>>  34   opls_140  1UNK 2H 21  0.146500
>> 1.00800
>>  35   opls_140  1UNK 3H 21  0.148972
>> 1.00800
>>  36   opls_140  1UNK  H 21  0.103605
>> 1.00800
>>  37   opls_140  1UNK  H 21  0.127061
>> 1.00800
>>  38   opls_140  1UNK 1H 21  0.143100
>> 1.0

Re: [gmx-users] topology

[Jakub Krajniak]

Did you try mktop ? (http://www.aribeiro.net.br/mktop)


On 02.03.2017 05:23, RAHUL SURESH wrote:

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:



On 3/1/17 2:19 PM, RAHUL SURESH wrote:


Dear Justin

What is the error here?
I don't understand it.
Can you be little more precise?



The long and short of it TopolGen is very crudely coded and atom order
matters because the script makes a lot of assumptions.  Your input PDB file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:



On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)

I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters

should be. It's pretty limited in what it can do.  A coordinate file that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
  1   opls_154  1UNK  O  0 -0.580921
15.99940
  2   opls_154  1UNK  O  0 -0.635654
15.99940
  3   opls_516  1UNK  C  1 -0.112257
12.01100
  4   opls_516  1UNK  C  2 -0.163224
12.01100
  5   opls_516  1UNK  C  3  0.228741
12.01100
  6   opls_516  1UNK  C  4 -0.304756
12.01100
  7   opls_516  1UNK  C  5 -0.312217
12.01100
  8   opls_145  1UNK  C  6  0.120569
12.01100
  9   opls_145  1UNK  C  7  0.151897
12.01100
 10   opls_145  1UNK  C  8  0.231044
12.01100
 11   opls_516  1UNK  C  9 -0.401751
12.01100
 12   opls_516  1UNK  C 10 -0.403094
12.01100
 13   opls_145  1UNK  C 11 -0.150352
12.01100
 14   opls_145  1UNK  C 12  0.193129
12.01100
 15   opls_145  1UNK  C 13 -0.161115
12.01100
 16   opls_516  1UNK  C 14 -0.471874
12.01100
 17   opls_145  1UNK  C 15  0.100725
12.01100
 18   opls_145  1UNK  C 16 -0.153943
12.01100
 19   opls_516  1UNK  C 17 -0.330577
12.01100
 20   opls_516  1UNK  C 18 -0.229875
12.01100
 21   opls_135  1UNK  C 19 -0.229884
12.01100
 22   opls_135  1UNK  C 20 -0.237230
12.01100
 23   opls_135  1UNK  C 21 -0.404861
12.01100
 24   opls_140  1UNK  H 21  0.135257
1.00800
 25   opls_140  1UNK  H 21  0.154010
1.00800
 26   opls_140  1UNK 2H 21  0.142643
1.00800
 27   opls_140  1UNK 1H 21  0.133623
1.00800
 28   opls_140  1UNK 2H 21  0.137323
1.00800
 29   opls_140  1UNK 1H 21  0.167475
1.00800
 30   opls_140  1UNK 1H 21  0.135348
1.00800
 31   opls_140  1UNK 2H 21  0.153851
1.00800
 32   opls_140  1UNK 3H 21  0.138487
1.00800
 33   opls_140  1UNK 1H 21  0.137087
1.00800
 34   opls_140  1UNK 2H 21  0.146500
1.00800
 35   opls_140  1UNK 3H 21  0.148972
1.00800
 36   opls_140  1UNK  H 21  0.103605
1.00800
 37   opls_140  1UNK  H 21  0.127061
1.00800
 38   opls_140  1UNK 1H 21  0.143100
1.00800
 39   opls_140  1UNK 2H 21  0.137525
1.00800
 40   opls_140  1UNK 3H 21  0.140672
1.00800
 41   opls_140  1UNK  H 21  0.106416
1.00800
 42   opls_140  1UNK 1H 21  0.134610
1.00800
 43   opls_140  1UNK 2H 21  0.126890
1.00800
 44   opls_140  1UNK 2H 21  0.132690
1.00800
 45   opls_140  1UNK 1H 21  0.124796
1.00800
 46   opls_140  1UNK  H 21  0.371894
1.00800
 47   opls_140  1UNK 1H 21  0.120642
1.00800
 48   opls_140  1UNK 2H 21  0.117792
1.00800
 49   opls_140  1UNK 2H 21  0.125342
1.00800
 50   opls_140  1UNK 1H 21  0.122930
1.00800
 51   opls_140  1UNK 1H 21  0.130012
1.00800
 52   opls_140  1UNK 2H 21  0.129674
1.00800
 53   opls_140  1UNK 3H 21  0.131255
1

Re: [gmx-users] topology

[Justin Lemkul]

On 3/2/17 8:25 AM, RAHUL SURESH wrote:

How to edit the .hdb file



Start by reading the manual section dedicated to .hdb files.

-Justin


On Thu, Mar 2, 2017 at 6:52 PM, RAHUL SURESH 
wrote:


I can manually parametrize my topology but to parametrize Hydrogen atoms
goes too tedious.
There must be any easy way.?

On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul  wrote:




On 3/2/17 2:51 AM, Subashini .K wrote:


Did you try PRODRG server?



Broken record time: the quality of PRODRG topologies is very low.  One
should always manually reparametrize the molecule, or use better servers
like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if
the goal is an OPLS-AA topology.

-Justin






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
SURESH 
Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] topology

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:




On 3/1/17 2:19 PM, RAHUL SURESH wrote:

Dear Justin


What is the error here?
I don't understand it.
Can you be little more precise?


The long and short of it TopolGen is very crudely coded and atom order

matters because the script makes a lot of assumptions.  Your input PDB
file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:






On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)



I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters


should be. It's pretty limited in what it can do.  A coordinate file
that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]


;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_154  1UNK  O  0 -0.580921
15.99940
 2   opls_154  1UNK  O  0 -0.635654
15.99940
 3   opls_516  1UNK  C  1 -0.112257
12.01100
 4   opls_516  1UNK  C  2 -0.163224
12.01100
 5   opls_516  1UNK  C  3  0.228741
12.01100
 6   opls_516  1UNK  C  4 -0.304756
12.01100
 7   opls_516  1UNK  C  5 -0.312217
12.01100
 8   opls_145  1UNK  C  6  0.120569
12.01100
 9   opls_145  1UNK  C  7  0.151897
12.01100
10   opls_145  1UNK  C  8  0.231044
12.01100
11   opls_516  1UNK  C  9 -0.401751
12.01100
12   opls_516  1UNK  C 10 -0.403094
12.01100
13   opls_145  1UNK  C 11 -0.150352
12.01100
14   opls_145  1UNK  C 12  0.193129
12.01100
15   opls_145  1UNK  C 13 -0.161115
12.01100
16   opls_516  1UNK  C 14 -0.471874
12.01100
17   opls_145  1UNK  C 15  0.100725
12.01100
18   opls_145  1UNK  C 16 -0.153943
12.01100
19   opls_516  1UNK  C 17 -0.330577
12.01100
20   opls_516  1UNK  C 18 -0.229875
12.01100
21   opls_135  1UNK  C 19 -0.229884
12.01100
22   opls_135  1UNK  C 20 -0.237230
12.01100
23   opls_135  1UNK  C 21 -0.404861
12.01100
24   opls_140  1UNK  H 21  0.135257
1.00800
25   opls_140  1UNK  H 21  0.154010
1.00800
26   opls_140  1UNK 2H 21  0.142643
1.00800
27   opls_140  1UNK 1H 21  0.133623
1.00800
28   opls_140  1UNK 2H 21  0.137323
1.00800
29   opls_140  1UNK 1H 21  0.167475
1.00800
30   opls_140  1UNK 1H 21  0.135348
1.00800
31   opls_140  1UNK 2H 21  0.153851
1.00800
32   opls_140  1UNK 3H 21  0.138487
1.00800
33   opls_140  1UNK 1H 21  0.137087
1.00800
34   opls_140  1UNK 2H 21  0.146500
1.00800
35   opls_140  1UNK 3H 21  0.148972
1.00800
36   opls_140  1UNK  H 21  0.103605
1.00800
37   opls_140  1UNK  H 21  0.127061
1.00800
38   opls_140  1UNK 1H 21  0.143100
1.00800
39   opls_140  1UNK 2H 21  0.137525
1.00800
40   opls_140  1UNK 3H 21  0.140672
1.00800
41   opls_140  1UNK  H

Re: [gmx-users] topology

[Justin Lemkul]

On 3/2/17 8:22 AM, RAHUL SURESH wrote:

I can manually parametrize my topology but to parametrize Hydrogen atoms
goes too tedious.
There must be any easy way.?



Take parameters (types and charges) by analogy from the existing force field. 
Validate against whatever experimental evidence or QM data you may have.


-Justin


On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul  wrote:




On 3/2/17 2:51 AM, Subashini .K wrote:


Did you try PRODRG server?



Broken record time: the quality of PRODRG topologies is very low.  One
should always manually reparametrize the molecule, or use better servers
like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if
the goal is an OPLS-AA topology.

-Justin






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
SURESH 
Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] topology

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:




On 3/1/17 2:19 PM, RAHUL SURESH wrote:

Dear Justin


What is the error here?
I don't understand it.
Can you be little more precise?


The long and short of it TopolGen is very crudely coded and atom order

matters because the script makes a lot of assumptions.  Your input PDB
file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:






On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)



I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters


should be. It's pretty limited in what it can do.  A coordinate file
that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]


;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_154  1UNK  O  0 -0.580921
15.99940
 2   opls_154  1UNK  O  0 -0.635654
15.99940
 3   opls_516  1UNK  C  1 -0.112257
12.01100
 4   opls_516  1UNK  C  2 -0.163224
12.01100
 5   opls_516  1UNK  C  3  0.228741
12.01100
 6   opls_516  1UNK  C  4 -0.304756
12.01100
 7   opls_516  1UNK  C  5 -0.312217
12.01100
 8   opls_145  1UNK  C  6  0.120569
12.01100
 9   opls_145  1UNK  C  7  0.151897
12.01100
10   opls_145  1UNK  C  8  0.231044
12.01100
11   opls_516  1UNK  C  9 -0.401751
12.01100
12   opls_516  1UNK  C 10 -0.403094
12.01100
13   opls_145  1UNK  C 11 -0.150352
12.01100
14   opls_145  1UNK  C 12  0.193129
12.01100
15   opls_145  1UNK  C 13 -0.161115
12.01100
16   opls_516  1UNK  C 14 -0.471874
12.01100
17   opls_145  1UNK  C 15  0.100725
12.01100
18   opls_145  1UNK  C 16 -0.153943
12.01100
19   opls_516  1UNK  C 17 -0.330577
12.01100
20   opls_516  1UNK  C 18 -0.229875
12.01100
21   opls_135  1UNK  C 19 -0.229884
12.01100
22   opls_135  1UNK  C 20 -0.237230
12.01100
23   opls_135  1UNK  C 21 -0.404861
12.01100
24   opls_140  1UNK  H 21  0.135257
1.00800
25   opls_140  1UNK  H 21  0.154010
1.00800
26   opls_140  1UNK 2H 21  0.142643
1.00800
27   opls_140  1UNK 1H 21  0.133623
1.00800
28   opls_140  1UNK 2H 21  0.137323
1.00800
29   opls_140  1UNK 1H 21  0.167475
1.00800
30   opls_140  1UNK 1H 21  0.135348
1.00800
31   opls_140  1UNK 2H 21  0.153851
1.00800
32   opls_140  1UNK 3H 21  0.138487
1.00800
33   opls_140  1UNK 1H 21  0.137087
1.00800
34   opls_140  1UNK 2H 21  0.146500
1.00800
35   opls_140  1UNK 3H 21  0.148972
1.00800
36   opls_140  1UNK  H 21  0.103605
1.00800
37   opls_140  1UNK  H 21  0.127061
1.00800
38   opls_140  1UNK 1H 21  0.143100
1.00800
39   opls_140  1UNK 2H 21  0.137525
1.00800
40   opls_140  1UNK 3H 21  0.140672
1.00800
41   opls_140  1

Re: [gmx-users] topology

[RAHUL SURESH]

How to edit the .hdb file

On Thu, Mar 2, 2017 at 6:52 PM, RAHUL SURESH 
wrote:

> I can manually parametrize my topology but to parametrize Hydrogen atoms
> goes too tedious.
> There must be any easy way.?
>
> On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 3/2/17 2:51 AM, Subashini .K wrote:
>>
>>> Did you try PRODRG server?
>>>
>>>
>> Broken record time: the quality of PRODRG topologies is very low.  One
>> should always manually reparametrize the molecule, or use better servers
>> like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if
>> the goal is an OPLS-AA topology.
>>
>> -Justin
>>
>>
>>
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
>>> SURESH 
>>> Sent: Thursday, March 2, 2017 9:53 AM
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] topology
>>>
>>> Dear Justin
>>>
>>> Is there anything I can do to make this job easier?
>>>
>>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:
>>>
>>>

 On 3/1/17 2:19 PM, RAHUL SURESH wrote:

 Dear Justin
>
> What is the error here?
> I don't understand it.
> Can you be little more precise?
>
>
> The long and short of it TopolGen is very crudely coded and atom order
 matters because the script makes a lot of assumptions.  Your input PDB
 file
 has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
 out what any of the actual functional groups are, so you get basically
 default atom types for everything.

 -Justin


 On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:

>
>
>
>> On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>>
>> This is my itp file(only a part)
>>
>>>
>>> I have highlighted two errors.. there are 19 such errors.
>>> If I can know the reason for the error exactly it would be of a great
>>> help
>>> to me.
>>>
>>>
>>> TopolGen relies on atom ordering to guess what the proper parameters
>>>
>> should be. It's pretty limited in what it can do.  A coordinate file
>> that
>> simply groups atoms by element is going to produce a totally garbage
>> topology, unfortunately.
>>
>> -Justin
>>
>>
>> [ atoms ]
>>
>>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>>> typeBchargeB  massB
>>>  1   opls_154  1UNK  O  0 -0.580921
>>> 15.99940
>>>  2   opls_154  1UNK  O  0 -0.635654
>>> 15.99940
>>>  3   opls_516  1UNK  C  1 -0.112257
>>> 12.01100
>>>  4   opls_516  1UNK  C  2 -0.163224
>>> 12.01100
>>>  5   opls_516  1UNK  C  3  0.228741
>>> 12.01100
>>>  6   opls_516  1UNK  C  4 -0.304756
>>> 12.01100
>>>  7   opls_516  1UNK  C  5 -0.312217
>>> 12.01100
>>>  8   opls_145  1UNK  C  6  0.120569
>>> 12.01100
>>>  9   opls_145  1UNK  C  7  0.151897
>>> 12.01100
>>> 10   opls_145  1UNK  C  8  0.231044
>>> 12.01100
>>> 11   opls_516  1UNK  C  9 -0.401751
>>> 12.01100
>>> 12   opls_516  1UNK  C 10 -0.403094
>>> 12.01100
>>> 13   opls_145  1UNK  C 11 -0.150352
>>> 12.01100
>>> 14   opls_145  1UNK  C 12  0.193129
>>> 12.01100
>>> 15   opls_145  1UNK  C 13 -0.161115
>>> 12.01100
>>> 16   opls_516  1UNK  C 14 -0.471874
>>> 12.01100
>>> 17   opls_145  1UNK  C 15  0.100725
>>> 12.01100
>>> 18   opls_145  1UNK  C 16 -0.153943
>>> 12.01100
>>> 19   opls_516  1UNK  C 17 -0.330577
>>> 12.01100
>>> 20   opls_516  1UNK  C 18 -0.229875
>>> 12.01100
>>> 21   opls_135  1UNK  C 19 -0.229884
>>> 12.01100
>>> 22   opls_135  1UNK  C 20 -0.237230
>>> 12.01100
>>> 23   opls_135  1UNK  C 21 -0.404861
>>> 12.01100
>>> 24   opls_140  1UNK  H 21  0.135257
>>> 1.00800
>>> 25   opls_140  1UNK  H 21  0.154010
>>> 1.00800
>>> 26   opls_140  1UNK 2H 21  0.142643
>>> 1.00800
>>> 27   opls_140  1UNK 1H 21  0.133623
>>> 1.00800
>>> 28   opls_140  1UNK 2H 21  0.137323
>>> 1.00800
>>> 29   opls_140  1UNK 1H 21  0.167475
>>> 1.00800
>>> 30   opls_140  1UNK

Re: [gmx-users] topology

[RAHUL SURESH]

I can manually parametrize my topology but to parametrize Hydrogen atoms
goes too tedious.
There must be any easy way.?

On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul  wrote:

>
>
> On 3/2/17 2:51 AM, Subashini .K wrote:
>
>> Did you try PRODRG server?
>>
>>
> Broken record time: the quality of PRODRG topologies is very low.  One
> should always manually reparametrize the molecule, or use better servers
> like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if
> the goal is an OPLS-AA topology.
>
> -Justin
>
>
>
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
>> SURESH 
>> Sent: Thursday, March 2, 2017 9:53 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] topology
>>
>> Dear Justin
>>
>> Is there anything I can do to make this job easier?
>>
>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>>>
>>> Dear Justin

 What is the error here?
 I don't understand it.
 Can you be little more precise?


 The long and short of it TopolGen is very crudely coded and atom order
>>> matters because the script makes a lot of assumptions.  Your input PDB
>>> file
>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
>>> out what any of the actual functional groups are, so you get basically
>>> default atom types for everything.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:
>>>



> On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>
> This is my itp file(only a part)
>
>>
>> I have highlighted two errors.. there are 19 such errors.
>> If I can know the reason for the error exactly it would be of a great
>> help
>> to me.
>>
>>
>> TopolGen relies on atom ordering to guess what the proper parameters
>>
> should be. It's pretty limited in what it can do.  A coordinate file
> that
> simply groups atoms by element is going to produce a totally garbage
> topology, unfortunately.
>
> -Justin
>
>
> [ atoms ]
>
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>> typeBchargeB  massB
>>  1   opls_154  1UNK  O  0 -0.580921
>> 15.99940
>>  2   opls_154  1UNK  O  0 -0.635654
>> 15.99940
>>  3   opls_516  1UNK  C  1 -0.112257
>> 12.01100
>>  4   opls_516  1UNK  C  2 -0.163224
>> 12.01100
>>  5   opls_516  1UNK  C  3  0.228741
>> 12.01100
>>  6   opls_516  1UNK  C  4 -0.304756
>> 12.01100
>>  7   opls_516  1UNK  C  5 -0.312217
>> 12.01100
>>  8   opls_145  1UNK  C  6  0.120569
>> 12.01100
>>  9   opls_145  1UNK  C  7  0.151897
>> 12.01100
>> 10   opls_145  1UNK  C  8  0.231044
>> 12.01100
>> 11   opls_516  1UNK  C  9 -0.401751
>> 12.01100
>> 12   opls_516  1UNK  C 10 -0.403094
>> 12.01100
>> 13   opls_145  1UNK  C 11 -0.150352
>> 12.01100
>> 14   opls_145  1UNK  C 12  0.193129
>> 12.01100
>> 15   opls_145  1UNK  C 13 -0.161115
>> 12.01100
>> 16   opls_516  1UNK  C 14 -0.471874
>> 12.01100
>> 17   opls_145  1UNK  C 15  0.100725
>> 12.01100
>> 18   opls_145  1UNK  C 16 -0.153943
>> 12.01100
>> 19   opls_516  1UNK  C 17 -0.330577
>> 12.01100
>> 20   opls_516  1UNK  C 18 -0.229875
>> 12.01100
>> 21   opls_135  1UNK  C 19 -0.229884
>> 12.01100
>> 22   opls_135  1UNK  C 20 -0.237230
>> 12.01100
>> 23   opls_135  1UNK  C 21 -0.404861
>> 12.01100
>> 24   opls_140  1UNK  H 21  0.135257
>> 1.00800
>> 25   opls_140  1UNK  H 21  0.154010
>> 1.00800
>> 26   opls_140  1UNK 2H 21  0.142643
>> 1.00800
>> 27   opls_140  1UNK 1H 21  0.133623
>> 1.00800
>> 28   opls_140  1UNK 2H 21  0.137323
>> 1.00800
>> 29   opls_140  1UNK 1H 21  0.167475
>> 1.00800
>> 30   opls_140  1UNK 1H 21  0.135348
>> 1.00800
>> 31   opls_140  1UNK 2H 21  0.153851
>> 1.00800
>> 32   opls_140  1UNK 3H 21  0.138487
>> 1.00800
>> 33   opls_140

Re: [gmx-users] Fatal error: Atomtype CA not found

[Justin Lemkul]

On 3/2/17 5:13 AM, Puneet wrote:

Hi,



I am performing Membrane protein simulation by using Bevan Tutorial "KALP15
in DPPC" with example given in tutorial. I have made steps upto "To use
parameters in lipid.itp, we will have to make some changes to our
pre-packaged gromos53a6.ff/forcefield.itp. Make a new directory in your
working directory called "gromos53a6_lipid.ff" and copy the following files
from gromos53a6.ff into it" and kept all the files in gromos53a6_lipid.ff
directory as mention under this section. I have also made all the required
changes in "ffnonbonded.itp & topol.top" as mention in the tutorial and
taken minim.mdp & topol_dppc.top files from link given in the tutorial. But
on step "Orient the protein and membrane" when I run



Command: grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr


I got  Fatal error: Atomtype CA not found

Can u please suggest me how to resolve this error.



You deleted too many things from ffnonbonded.itp.  Start over, and follow 
instructions closely.


-Justin



Thanks in Advance!


Regards!


Puneet



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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Re: [gmx-users] topology

[Justin Lemkul]

On 3/2/17 2:51 AM, Subashini .K wrote:

Did you try PRODRG server?



Broken record time: the quality of PRODRG topologies is very low.  One should 
always manually reparametrize the molecule, or use better servers like ATB. 
PRODRG and ATB produce GROMOS topologies, which are not useful if the goal is an 
OPLS-AA topology.


-Justin





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of RAHUL SURESH 

Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] topology

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:




On 3/1/17 2:19 PM, RAHUL SURESH wrote:


Dear Justin

What is the error here?
I don't understand it.
Can you be little more precise?



The long and short of it TopolGen is very crudely coded and atom order
matters because the script makes a lot of assumptions.  Your input PDB file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:





On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)


I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters

should be. It's pretty limited in what it can do.  A coordinate file that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_154  1UNK  O  0 -0.580921
15.99940
 2   opls_154  1UNK  O  0 -0.635654
15.99940
 3   opls_516  1UNK  C  1 -0.112257
12.01100
 4   opls_516  1UNK  C  2 -0.163224
12.01100
 5   opls_516  1UNK  C  3  0.228741
12.01100
 6   opls_516  1UNK  C  4 -0.304756
12.01100
 7   opls_516  1UNK  C  5 -0.312217
12.01100
 8   opls_145  1UNK  C  6  0.120569
12.01100
 9   opls_145  1UNK  C  7  0.151897
12.01100
10   opls_145  1UNK  C  8  0.231044
12.01100
11   opls_516  1UNK  C  9 -0.401751
12.01100
12   opls_516  1UNK  C 10 -0.403094
12.01100
13   opls_145  1UNK  C 11 -0.150352
12.01100
14   opls_145  1UNK  C 12  0.193129
12.01100
15   opls_145  1UNK  C 13 -0.161115
12.01100
16   opls_516  1UNK  C 14 -0.471874
12.01100
17   opls_145  1UNK  C 15  0.100725
12.01100
18   opls_145  1UNK  C 16 -0.153943
12.01100
19   opls_516  1UNK  C 17 -0.330577
12.01100
20   opls_516  1UNK  C 18 -0.229875
12.01100
21   opls_135  1UNK  C 19 -0.229884
12.01100
22   opls_135  1UNK  C 20 -0.237230
12.01100
23   opls_135  1UNK  C 21 -0.404861
12.01100
24   opls_140  1UNK  H 21  0.135257
1.00800
25   opls_140  1UNK  H 21  0.154010
1.00800
26   opls_140  1UNK 2H 21  0.142643
1.00800
27   opls_140  1UNK 1H 21  0.133623
1.00800
28   opls_140  1UNK 2H 21  0.137323
1.00800
29   opls_140  1UNK 1H 21  0.167475
1.00800
30   opls_140  1UNK 1H 21  0.135348
1.00800
31   opls_140  1UNK 2H 21  0.153851
1.00800
32   opls_140  1UNK 3H 21  0.138487
1.00800
33   opls_140  1UNK 1H 21  0.137087
1.00800
34   opls_140  1UNK 2H 21  0.146500
1.00800
35   opls_140  1UNK 3H 21  0.148972
1.00800
36   opls_140  1UNK  H 21  0.103605
1.00800
37   opls_140  1UNK  H 21  0.127061
1.00800
38   opls_140  1UNK 1H 21  0.143100
1.00800
39   opls_140  1UNK 2H 21  0.137525
1.00800
40   opls_140  1UNK 3H 21  0.140672
1.00800
41   opls_140  1UNK  H 21  0.106416
1.00800
42   opls_140  1UNK 1H 21  0.134610
1.00800
43   opls_140  1UNK 2H 21  0.126890
1.00800
44   opls_140  1UNK 2H 21  0.132690
1.00800
45   opls_140  1UNK 1H 21  0.124796
1.00800
46   opls_140  1UNK  H 21  0.371894
1.00800
47   opls_140  1UNK 1H 21  0.1206

Re: [gmx-users] topology

[Justin Lemkul]

On 3/1/17 11:23 PM, RAHUL SURESH wrote:

Dear Justin

Is there anything I can do to make this job easier?



Generate the small molecule coordinates based on a better program that does not 
produce a difficult-to-use coordinate file, or choose a different force field 
that has parametrization tools that make your life easier.


-Justin


On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:




On 3/1/17 2:19 PM, RAHUL SURESH wrote:


Dear Justin

What is the error here?
I don't understand it.
Can you be little more precise?



The long and short of it TopolGen is very crudely coded and atom order
matters because the script makes a lot of assumptions.  Your input PDB file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:





On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)


I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters

should be. It's pretty limited in what it can do.  A coordinate file that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_154  1UNK  O  0 -0.580921
15.99940
 2   opls_154  1UNK  O  0 -0.635654
15.99940
 3   opls_516  1UNK  C  1 -0.112257
12.01100
 4   opls_516  1UNK  C  2 -0.163224
12.01100
 5   opls_516  1UNK  C  3  0.228741
12.01100
 6   opls_516  1UNK  C  4 -0.304756
12.01100
 7   opls_516  1UNK  C  5 -0.312217
12.01100
 8   opls_145  1UNK  C  6  0.120569
12.01100
 9   opls_145  1UNK  C  7  0.151897
12.01100
10   opls_145  1UNK  C  8  0.231044
12.01100
11   opls_516  1UNK  C  9 -0.401751
12.01100
12   opls_516  1UNK  C 10 -0.403094
12.01100
13   opls_145  1UNK  C 11 -0.150352
12.01100
14   opls_145  1UNK  C 12  0.193129
12.01100
15   opls_145  1UNK  C 13 -0.161115
12.01100
16   opls_516  1UNK  C 14 -0.471874
12.01100
17   opls_145  1UNK  C 15  0.100725
12.01100
18   opls_145  1UNK  C 16 -0.153943
12.01100
19   opls_516  1UNK  C 17 -0.330577
12.01100
20   opls_516  1UNK  C 18 -0.229875
12.01100
21   opls_135  1UNK  C 19 -0.229884
12.01100
22   opls_135  1UNK  C 20 -0.237230
12.01100
23   opls_135  1UNK  C 21 -0.404861
12.01100
24   opls_140  1UNK  H 21  0.135257
1.00800
25   opls_140  1UNK  H 21  0.154010
1.00800
26   opls_140  1UNK 2H 21  0.142643
1.00800
27   opls_140  1UNK 1H 21  0.133623
1.00800
28   opls_140  1UNK 2H 21  0.137323
1.00800
29   opls_140  1UNK 1H 21  0.167475
1.00800
30   opls_140  1UNK 1H 21  0.135348
1.00800
31   opls_140  1UNK 2H 21  0.153851
1.00800
32   opls_140  1UNK 3H 21  0.138487
1.00800
33   opls_140  1UNK 1H 21  0.137087
1.00800
34   opls_140  1UNK 2H 21  0.146500
1.00800
35   opls_140  1UNK 3H 21  0.148972
1.00800
36   opls_140  1UNK  H 21  0.103605
1.00800
37   opls_140  1UNK  H 21  0.127061
1.00800
38   opls_140  1UNK 1H 21  0.143100
1.00800
39   opls_140  1UNK 2H 21  0.137525
1.00800
40   opls_140  1UNK 3H 21  0.140672
1.00800
41   opls_140  1UNK  H 21  0.106416
1.00800
42   opls_140  1UNK 1H 21  0.134610
1.00800
43   opls_140  1UNK 2H 21  0.126890
1.00800
44   opls_140  1UNK 2H 21  0.132690
1.00800
45   opls_140  1UNK 1H 21  0.124796
1.00800
46   opls_140  1UNK  H 21  0.371894
1.00800
47   opls_140  1UNK 1H 21  0.120642
1.00800
48   opls_140  1UNK 2H 21  0.117792
1.00800
49   opls_140  1UNK 2H 21  0.125342
1.00800
50   opls_140  1UNK 1H 21  0.122930
1.00800
51   opls_140  1UNK 1H 21  0.130012
1.00800
 

Re: [gmx-users] Per lipid area for heterogeneous membrane

[Justin Lemkul]

On 3/2/17 1:09 AM, shweta singh wrote:

Hi Justin,

I have a vesicle system with whole in it (c-shpaed).  I want to calculate
the distance of open end of vesicle, but the lipids present on the top of
open end diffuses very much so it can not possible to calculate the
distance by any two atom of lipid molecule.

I want to calculate the distance between atoms of present on the top by
taking set of coordinate. How can I the fetch atoms giving the XYZ
coordinates and is there any command which calculate the distance by taking
the set of coordinate ?



You probably want some selection per frame using gmx select, but I don't 
understand your situation.


Please start a new thread if your question is unrelated to the original post so 
as not to hijack other topics.


-Justin



Thanks,
Shweta

On Thu, Mar 2, 2017 at 11:04 AM, Мижээ Батсайхан 
wrote:


Dear Justin,

Thank you very much for your reply. I have a further question about
GridMAT-MD tool. Is it possible to use in case with different upper leaflet
and lower leaflet? In the manual, GridMAT-MD tool needs the leaflet tails
face towards.

Best regards,
Mijee

On 3/1/17 8:56 AM, ? ? wrote:

Dear gmx users,

Hello, My simulation system consists of severil different type of

membrane

models including ergosterols. I want to analysis per lipid area for

this

system. How can I calculate the area? Please advice me.

Can I use GridMAT-MD tool? If it is possible, how I do.



Yes, and we provide an example of a mixed bilayer in section 7.2 of our
PDF manual.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Per lipid area for heterogeneous membrane

[Justin Lemkul]

On 3/2/17 12:34 AM, Мижээ Батсайхан wrote:

Dear Justin,

Thank you very much for your reply. I have a further question about
GridMAT-MD tool. Is it possible to use in case with different upper leaflet
and lower leaflet? In the manual, GridMAT-MD tool needs the leaflet tails
face towards.



We split the membrane based on the "middle" of the lipid coordinates, so "top" 
and "bottom" may be inverted if your membrane is, e.g. split across PBC.  But 
those designators are arbitrary anyway in a periodic system, so you just have to 
keep track of what is what.


-Justin


Best regards,
Mijee

On 3/1/17 8:56 AM, ? ? wrote:

Dear gmx users,

Hello, My simulation system consists of severil different type of

membrane

models including ergosterols. I want to analysis per lipid area for this
system. How can I calculate the area? Please advice me.

Can I use GridMAT-MD tool? If it is possible, how I do.



Yes, and we provide an example of a mixed bilayer in section 7.2 of our
PDF manual.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] MM/Pbsa

[Kingsley Theras Primus Dass .]

Hi,
 I tried to calculate binding free energy for my protein. I tried using MM
/ PBSA, when i ran the program i am getting an error. Could you please say
why such error is occuring and how should i need to rectify it.



the error message is below


17:54:41
 The directory RUN_ is not present. Please check the INPUT.dat file or run
"gmxpbsa0.pbs".
Exiting -


Thank you.

Kingsley Theras
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[gmx-users] Fatal error: Atomtype CA not found

[Puneet]

Hi, 

 

I am performing Membrane protein simulation by using Bevan Tutorial "KALP15
in DPPC" with example given in tutorial. I have made steps upto "To use
parameters in lipid.itp, we will have to make some changes to our
pre-packaged gromos53a6.ff/forcefield.itp. Make a new directory in your
working directory called "gromos53a6_lipid.ff" and copy the following files
from gromos53a6.ff into it" and kept all the files in gromos53a6_lipid.ff
directory as mention under this section. I have also made all the required
changes in "ffnonbonded.itp & topol.top" as mention in the tutorial and
taken minim.mdp & topol_dppc.top files from link given in the tutorial. But
on step "Orient the protein and membrane" when I run 

 

Command: grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

 
I got  Fatal error: Atomtype CA not found

Can u please suggest me how to resolve this error.


Thanks in Advance!


Regards!


Puneet

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Re: [gmx-users] Per lipid area for heterogeneous membrane

[Björn Sommer]

Dear Mijee,

alternatively to GridMat, you might also want to have a look at our
APL@Voro:

http://aplvoro.org

It provides a GUI, so you can easily import your PDB file into the tool
and analyze the APL, thickness and neighborhood based on Voronoi
tesselation. Later, you can also import trajectory files and analyze
them over time. The publication reference you will also find at the website.

Cheers,
Bjorn
 
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Re: [gmx-users] Gromacs with Plumed

[Giovanni Bussi]

Hi,

I am not aware of problems, so in case you find any please report them.

If you want to simplify the installation setup, also consider the "patch
--runtime" option. Coupled with env modules, it allows you to upgrade
gromacs and plumed independently and to combine them arbitrarily

Giovanni


On Thu, Mar 2, 2017 at 9:09 AM, Åke Sandgren 
wrote:

> Hi!
>
> Are there any known drawbacks to building Gromacs with Plumed?
>
> I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
> both if there are problems with any version combination i'd like to know
> that too.
>
> I.e., will it cause problems for non-plumed runs, will gromacs behave
> identical to a non-plumed build when not using plumed in the
> plumed-build, etc.?
>
> Having just a single build makes my life easier :-)
>
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> --
> Gromacs Users mailing list
>
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> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>



-- 
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Scuola Internazionale Superiore di Studi Avanzati - SISSA
via Bonomea 265, 34136 Trieste, Italy
email: bu...@sissa.it
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  http://srnas.sissa.it
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[gmx-users] Gromacs with Plumed

[Åke Sandgren]

Hi!

Are there any known drawbacks to building Gromacs with Plumed?

I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
both if there are problems with any version combination i'd like to know
that too.

I.e., will it cause problems for non-plumed runs, will gromacs behave
identical to a non-plumed build when not using plumed in the
plumed-build, etc.?

Having just a single build makes my life easier :-)

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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