[gmx-users] Clustering based on other parameters than RMSD

[soumadwip ghosh]

Hi all,

Sorry about the last incomplete mail.I have a trajectory of 300 ns for a
membrane protein. I want to sample native/non-native conformations and
compare across various systems. My question is can parameters like
number/occupancy of hbonds or the time evolution of helical residues
(output from gmx do_dssp) be clustered using something like gmx cluster or
something similar? As far as I understand gmx cluster does RMSD/distance
RMSD clustering based on a predefined cut-off. I am trying to extract the
number of accessible microstates for a given system, extract the
corresponding trajectories and do some property analysis. This is to be
done based on proportion of native/non-native like states which may be
related to assigning partially denaturated state of the protein. I did
cluster analysis on PCA but it seems difficult to compare across different
systems since they have different principal components. I have plotted free
energy surfaces by taking the percentage helicity, number of hydrogen bonds
and their probability (using the gmx sham utility) as X, Y and Z variables
respectively and I am looking at different microstates. Is this approach
right or am I missing something?

I would appreciate any input on this regard.

Thanks and regards,
Soumadwip Ghosh
Post Doctoral Research Associate
Prof. Vaidehi Nagarajan's group
Department of Molecular Immunology
City of Hope Cancer Research Center
Duarte, CA 91010
United States
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[gmx-users] Clustering based on other parameters than RMSD

[soumadwip ghosh]

Hi all,

I have a trajectory of 300 ns for a membrane protein. I want to sample
native/non-native conformations and compare across various systems. My
question is can parameters like number/occupancy of hbonds or the time
evolution of helical residues (output from gmx do_dssp) be clusterized
using something like gmx cluster or something similar? As far as I
understand gmx cluster does RMSD/distance RMSD clustering based on a
predefined cut-off. I am trying to extract the number of accessible
microstates for a given system, extract the corresponding trajectories and
do some property analysis. This is to be done based on proportion of
native/non-native like states which may be related to assigning partially
denaturated state of the protein. I did cluster analysis on PCA but it
seems difficult to compare across different systems since they have
different principal components.
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[gmx-users] polarizable simulation

[limingru]

Hello Justin,   Thanks for your answer. So can ethanol molecule be 
supported by 2013-Drude force field in GMX, if any, how to get its itp file? 
Thanks a lot.



==Date: Thu, 26 Oct 2017 
07:08:33 -0400From: Justin Lemkul To: 
gmx-users@gromacs.orgSubject: Re: [gmx-users] Drude format fileMessage-ID: 
<10acc8bd-8e8a-5fcb-631f-1ad9db844...@vt.edu>Content-Type: text/plain; 
charset=utf-8; format=flowedOn 10/26/17 3:20 AM, limingru wrote:> Hi gmx users 
or developers, I am trying to do some Drude polarizable simulations using GMX. 
How to convert coordinate file (e.g pdb) into Drude format file? Thanks in 
advance.There is no special "Drude format" for coordinate files. If you're 
referring to building on Drudes and lone pairs, pdb2gmx does all of that for 
you.-Justin-- ==



School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  

E-mail: mr...@sina.com 
mr...@mail.bnu.edu.cn




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[gmx-users] Drug membrane simulation

[Chetan Puri]

I want to determine permeability of drug molecules through various lipid
membranes.
Building the membrane i am able to do with the kalp-dppc tutorial, but for
placing the drug molecule above the membrane i am not getting proper
solution.

So can someone suggest how to place the drug molecule above the membrane
which contains water also.

CHETAN
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Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

[Justin Lemkul]

On 10/26/17 1:58 PM, Hoa Trinh wrote:

Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.


Well, you'll find many of those in every software package, and 
n_elements_of_type_and_atom_index is harder to type than nbonds :)


An explanation of how things are laid out is in topology/ifunc.h:

/*
 * The struct t_ilist defines a list of atoms with their interactions.
 * General field description:
 *   int nr
 *  the size (nr elements) of the interactions array (iatoms[]).
 *   t_iatom *iatoms
 *  specifies which atoms are involved in an interaction of a certain
 *   type. The layout of this array is as follows:
 *
 * +-+---+---+---+-+---+---+-+---+---+---+-+---+---+...
 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 * +-+---+---+---+-+---+---+-+---+---+---+-+---+---+...
 *
 *  So for interaction type type1 3 atoms are needed, and for type2 and
 *  type3 only 2. The type identifier is used to select the function to
 *  calculate the interaction and its actual parameters. This type
 *  identifier is an index in a params[] and functype[] array.
 */

-Justin


*Lan Hoa*

2017-10-26 6:10 GMT-05:00 Justin Lemkul :



On 10/26/17 1:56 AM, Hoa Trinh wrote:


Hi all,
I am trying to look into the source code of Gromacs 5.0.7 to see how
Gromacs calculate bonded interactions. For example, to calculate bond
interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
real bonds(int nbonds, ...)
{

for (i = 0; (i < nbonds); )
  {
  type = forceatoms[i++];
  ai   = forceatoms[i++];
  aj   = forceatoms[i++];

}
Is "nbonds" the total number of bond interactions? In my topology file, I
have 126 pairs in the [ bonds ] section. However, when I printf the
variable nbonds, it appears to be 378. I have no idea why. Can anyone
please help me to explain what is nbonds?


378 = 126 * 3

nbonds here indicates the size of the array, which holds (type, ai, aj)
for each bond in the system.

-Justin

--
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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

[Hoa Trinh]

Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.

*Lan Hoa*

2017-10-26 6:10 GMT-05:00 Justin Lemkul :

>
>
> On 10/26/17 1:56 AM, Hoa Trinh wrote:
>
>> Hi all,
>> I am trying to look into the source code of Gromacs 5.0.7 to see how
>> Gromacs calculate bonded interactions. For example, to calculate bond
>> interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
>> real bonds(int nbonds, ...)
>> {
>>
>>for (i = 0; (i < nbonds); )
>>  {
>>  type = forceatoms[i++];
>>  ai   = forceatoms[i++];
>>  aj   = forceatoms[i++];
>> 
>> }
>> Is "nbonds" the total number of bond interactions? In my topology file, I
>> have 126 pairs in the [ bonds ] section. However, when I printf the
>> variable nbonds, it appears to be 378. I have no idea why. Can anyone
>> please help me to explain what is nbonds?
>>
>
> 378 = 126 * 3
>
> nbonds here indicates the size of the array, which holds (type, ai, aj)
> for each bond in the system.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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[gmx-users] viscosity from periodic perturbation method

[Faezeh Pousaneh]

Hi,

My simulation results for viscosity calculation strongly depends on the
chosen amplitudes of the acceleration profiles in the .mdp file (!?). How
to estimate acceleration amplitude values?

appreciate if someone can answer,
Best regards
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Re: [gmx-users] Gromacs 2016.4 - the Intel compiler and 'make check'

[Mark Dixon]

Thanks - good to know that there is no clear winner between GCC and Intel 
with GROMACS performance.


As I'm building the software on behalf of a number of other people, and so 
don't have a typical simulation to do speed tests with, I can happily pick 
the lower-risk option and switch to GCC.


Regards,

Mark

On Thu, 26 Oct 2017, Mark Abraham wrote:


Hi,

It might, but Intel also works on the gcc and llvm compilers and their core
business is hardware, not selling the compiler. Our experience on non-Phi
is that performance is often quite close, but your actual hardware and
simulation are probably also going to affect which compiler implementation
works fastest for you.

Mark

On Thu, 26 Oct 2017 17:10 Mark Dixon  wrote:


Hi Mark,

Many thanks for the reply.

Am I going against the flow by using the Intel compiler with GROMACS? I've
been using it so far because of - the potentially foolhardy idea - that it
might generate a faster executable than GCC on modern Intel processors.

Best,

Mark

On Thu, 26 Oct 2017, Mark Abraham wrote:


Hi,

Thanks for the report - we should look into that combination. It's highly
likely that there's some minor issue that different optimization

capability

is creating or exposing. The functionality covered by that test is only
used for a few analysis tools, and the fact that gcc passes fine suggests
you should be confident in the code and icc.

Mark

On Thu, 26 Oct 2017 13:56 Mark Dixon  wrote:


Hi there,

Is there a recommended compiler for GROMACS, please?

I'm trying to validate my install on a CentOS 7.4 Intel Broadwell system
by running the tests shipped in the GROMACS source tar ball (and the
separate regression tests).

If I use GCC (4.8.5 or 7.2.0), everything passes but, if I use the Intel
compilers (tested 16.0.2 and 17.0.1), it keeps failing on
CorrelationsTest. I've tried pruning it down to the minimum build:

   cmake ../gromacs-2016.4 -DGMX_BUILD_OWN_FFTW=ON
   make -j12
   make check

And I see the following:

16/27 Test #16: CorrelationsTest .***Exception:

Numerical

0.25 sec
[==] Running 20 tests from 2 test cases.
[--] Global test environment set-up.
[--] 10 tests from AutocorrTest
[ RUN  ] AutocorrTest.EacNormal
[   OK ] AutocorrTest.EacNormal (39 ms)
[ RUN  ] AutocorrTest.EacNoNormalize
[   OK ] AutocorrTest.EacNoNormalize (73 ms)
[ RUN  ] AutocorrTest.EacCos
[   OK ] AutocorrTest.EacCos (53 ms)
[ RUN  ] AutocorrTest.EacVector
[   OK ] AutocorrTest.EacVector (66 ms)
[ RUN  ] AutocorrTest.EacRcross

I delved into the build directory, hoping to find a log with a bit more
information and found the string 'Floating point exception', but nothing
more.

Any advice you can give would be appreciated!

Thanks,

Mark

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[gmx-users] Doubt about density of states from md trajectory

[Varvdekar Bhagyesh Rajendra]

Dear all,

I have found density of states (Dos) of a protein ligand system from gmx dos 
command of gromacs. I would like to know if it employs the same principle 
component analysis as used in g_covar. If not what are the differences. 

Also the Dos obtained from gmx dos has solid and diffusive components, please 
can anyone shed light on what are they exactly?

Thank you,

Bhagyesh

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Re: [gmx-users] Gromacs 2016.4 - the Intel compiler and 'make check'

[Mark Abraham]

Hi,

It might, but Intel also works on the gcc and llvm compilers and their core
business is hardware, not selling the compiler. Our experience on non-Phi
is that performance is often quite close, but your actual hardware and
simulation are probably also going to affect which compiler implementation
works fastest for you.

Mark

On Thu, 26 Oct 2017 17:10 Mark Dixon  wrote:

> Hi Mark,
>
> Many thanks for the reply.
>
> Am I going against the flow by using the Intel compiler with GROMACS? I've
> been using it so far because of - the potentially foolhardy idea - that it
> might generate a faster executable than GCC on modern Intel processors.
>
> Best,
>
> Mark
>
> On Thu, 26 Oct 2017, Mark Abraham wrote:
>
> > Hi,
> >
> > Thanks for the report - we should look into that combination. It's highly
> > likely that there's some minor issue that different optimization
> capability
> > is creating or exposing. The functionality covered by that test is only
> > used for a few analysis tools, and the fact that gcc passes fine suggests
> > you should be confident in the code and icc.
> >
> > Mark
> >
> > On Thu, 26 Oct 2017 13:56 Mark Dixon  wrote:
> >
> >> Hi there,
> >>
> >> Is there a recommended compiler for GROMACS, please?
> >>
> >> I'm trying to validate my install on a CentOS 7.4 Intel Broadwell system
> >> by running the tests shipped in the GROMACS source tar ball (and the
> >> separate regression tests).
> >>
> >> If I use GCC (4.8.5 or 7.2.0), everything passes but, if I use the Intel
> >> compilers (tested 16.0.2 and 17.0.1), it keeps failing on
> >> CorrelationsTest. I've tried pruning it down to the minimum build:
> >>
> >>cmake ../gromacs-2016.4 -DGMX_BUILD_OWN_FFTW=ON
> >>make -j12
> >>make check
> >>
> >> And I see the following:
> >>
> >> 16/27 Test #16: CorrelationsTest .***Exception:
> Numerical
> >> 0.25 sec
> >> [==] Running 20 tests from 2 test cases.
> >> [--] Global test environment set-up.
> >> [--] 10 tests from AutocorrTest
> >> [ RUN  ] AutocorrTest.EacNormal
> >> [   OK ] AutocorrTest.EacNormal (39 ms)
> >> [ RUN  ] AutocorrTest.EacNoNormalize
> >> [   OK ] AutocorrTest.EacNoNormalize (73 ms)
> >> [ RUN  ] AutocorrTest.EacCos
> >> [   OK ] AutocorrTest.EacCos (53 ms)
> >> [ RUN  ] AutocorrTest.EacVector
> >> [   OK ] AutocorrTest.EacVector (66 ms)
> >> [ RUN  ] AutocorrTest.EacRcross
> >>
> >> I delved into the build directory, hoping to find a log with a bit more
> >> information and found the string 'Floating point exception', but nothing
> >> more.
> >>
> >> Any advice you can give would be appreciated!
> >>
> >> Thanks,
> >>
> >> Mark
> >> --
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Re: [gmx-users] Restraining one water molecule - settles vs constraints

[Justin Lemkul]

On 10/26/17 10:13 AM, Hermann, Johannes wrote:

Hi Justin,

yes everything is clear in the manual.

What I now get are lincs warnings for the OW-HW1 and OW-HW2 bond:

(exemplary for the OW-HW1 bond):

LINCS WARNING in simulation 1
relative constraint deviation after LINCS:
rms 0.317574, max 0.547778 (between atoms 1 and 2)
bonds that rotated more than 30 degrees:

Corresponding lincs parameters in the mdp file:

; options for bonds
constraints  = h-bonds
constraint-algorithm = lincs
lincs-order  = 4

Do I have to change anything else in the itp file for my "special" 
water (which I generated from tip3p.itp)? Currently I only changed the 
[ settles ] - section into the [ constraints ] section.




The approach you outlined should work fine. The LINCS warning just 
indicates that whatever else you're trying to do is unstable.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] No default Proper Dih. types when using neutral terminal

[Justin Lemkul]

On 10/26/17 10:09 AM, Simon Kit Sang Chu wrote:

Hi everyone,

Last time, I mentioned missing parameter for neutral terminal dihedral and
U-B type. After some debugging, I am still not sure what the cause was. I
hope providing more information could help to resolve the issue. I am using
CHARMM36 forcefield.

Brief summary of the problem -
No dihed. parameter / U-B types after using neutral terminals

Command I ran -

1. gmx pdb2gmx -f ALA-GLY-GLY-PRO. pdb -o ALA-GLY-GLY-PRO.gro -p
ALA-GLY-GLY-PRO.top -i ALA-GLY-GLY-PRO.itp -water tip3p -ignh -ter
Choose CHARMM36 all-atom force field (November 2016), NH2 and COOH
terminals


Note that the combination of NH2 and COOH cannot occur at any real pH 
value, so choose wisely what you're doing...



2. gmx editconf -f ALA-GLY-GLY-PRO.gro -o ALA-GLY-GLY-PRO-box.gro -c -d
0.8 -bt dodecahedron
3. gmx solvate -cp ALA-GLY-GLY-PRO-box.gro -cs spc216.gro -o
ALA-GLY-GLY-PRO-solvated.gro -p ALA-GLY-GLY-PRO.top
4. gmx grompp -f ions.mdp -c ALA-GLY-GLY-PRO-solvated.gro -p
ALA-GLY-GLY-PRO.top -o ions.tpr

Fatal error in grompp -


ERROR 1 [file ALA-GLY-GLY-PRO.top, line 293]:
   No default U-B types

ERROR 2 [file ALA-GLY-GLY-PRO.top, line 367]:
   No default Proper Dih. types
Meanwhile in the topology file -

[ angles ]

303840 5  ( line 293 )


[ dihedral ]

27263038 9  ( line 367 )


These are indeed missing parameters in the CHARMM force field, derived 
from the fact that the CA atom type is different in PRO than any other 
amino acid. Probably no one has ever needed to do a simulation of a 
system like this so no one ever ran into it. You can probably safely 
assign parameters by analogy using anything that has CT1 instead of CP1, 
which is the CA type in PRO.


-Justin


; residue   5 PRO rtp PRO  q  0.0
 26  N  5PRO  N 26  -0.29 14.007   ;
qtot -0.29
 27CP3  5PRO CD 27  0 12.011   ;
qtot -0.29
 28HA2  5PROHD1 28   0.09  1.008   ;
qtot -0.2
 29HA2  5PROHD2 29   0.09  1.008   ;
qtot -0.11
 30CP1  5PRO CA 30   0.02 12.011   ;
qtot -0.09
 31HB1  5PRO HA 31   0.09  1.008   ;
qtot 0
 32CP2  5PRO CB 32  -0.18 12.011   ;
qtot -0.18
 33HA2  5PROHB1 33   0.09  1.008   ;
qtot -0.09
 34HA2  5PROHB2 34   0.09  1.008   ;
qtot 0
 35CP2  5PRO CG 35  -0.18 12.011   ;
qtot -0.18
 36HA2  5PROHG1 36   0.09  1.008   ;
qtot -0.09
 37HA2  5PROHG2 37   0.09  1.008   ;
qtot 0
 38 CD  5PRO  C 38   0.72 12.011   ;
qtot 0.72
 39 OB  5PROOT1 39  -0.5515.9994   ;
qtot 0.17
 40OH1  5PROOT2 40  -0.6115.9994   ;
qtot -0.44
 41  H  5PROHT2 41   0.44  1.008   ;
qtot 0


I further check if angle type between CP1, CD and OH1 exists in ffbond.itp.
Indeed there is no such angle.  Maybe there is something wrong when using
NH2 and COOH terminals?

Please feel free to give any suggestion. I appreciate any comment.

Regards,
Simon


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Gromacs 2016.4 - the Intel compiler and 'make check'

[Mark Dixon]

Hi Mark,

Many thanks for the reply.

Am I going against the flow by using the Intel compiler with GROMACS? I've 
been using it so far because of - the potentially foolhardy idea - that it 
might generate a faster executable than GCC on modern Intel processors.


Best,

Mark

On Thu, 26 Oct 2017, Mark Abraham wrote:


Hi,

Thanks for the report - we should look into that combination. It's highly
likely that there's some minor issue that different optimization capability
is creating or exposing. The functionality covered by that test is only
used for a few analysis tools, and the fact that gcc passes fine suggests
you should be confident in the code and icc.

Mark

On Thu, 26 Oct 2017 13:56 Mark Dixon  wrote:


Hi there,

Is there a recommended compiler for GROMACS, please?

I'm trying to validate my install on a CentOS 7.4 Intel Broadwell system
by running the tests shipped in the GROMACS source tar ball (and the
separate regression tests).

If I use GCC (4.8.5 or 7.2.0), everything passes but, if I use the Intel
compilers (tested 16.0.2 and 17.0.1), it keeps failing on
CorrelationsTest. I've tried pruning it down to the minimum build:

   cmake ../gromacs-2016.4 -DGMX_BUILD_OWN_FFTW=ON
   make -j12
   make check

And I see the following:

16/27 Test #16: CorrelationsTest .***Exception: Numerical
0.25 sec
[==] Running 20 tests from 2 test cases.
[--] Global test environment set-up.
[--] 10 tests from AutocorrTest
[ RUN  ] AutocorrTest.EacNormal
[   OK ] AutocorrTest.EacNormal (39 ms)
[ RUN  ] AutocorrTest.EacNoNormalize
[   OK ] AutocorrTest.EacNoNormalize (73 ms)
[ RUN  ] AutocorrTest.EacCos
[   OK ] AutocorrTest.EacCos (53 ms)
[ RUN  ] AutocorrTest.EacVector
[   OK ] AutocorrTest.EacVector (66 ms)
[ RUN  ] AutocorrTest.EacRcross

I delved into the build directory, hoping to find a log with a bit more
information and found the string 'Floating point exception', but nothing
more.

Any advice you can give would be appreciated!

Thanks,

Mark
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Re: [gmx-users] No default Proper Dih. types when using neutral terminal

[Mark Abraham]

Hi,

I would look back to the literature to find what terminal PRO has CMAP
defined.

Mark

On Thu, 26 Oct 2017 16:10 Simon Kit Sang Chu  wrote:

> Hi everyone,
>
> Last time, I mentioned missing parameter for neutral terminal dihedral and
> U-B type. After some debugging, I am still not sure what the cause was. I
> hope providing more information could help to resolve the issue. I am using
> CHARMM36 forcefield.
>
> Brief summary of the problem -
> No dihed. parameter / U-B types after using neutral terminals
>
> Command I ran -
>
>1. gmx pdb2gmx -f ALA-GLY-GLY-PRO. pdb -o ALA-GLY-GLY-PRO.gro -p
>ALA-GLY-GLY-PRO.top -i ALA-GLY-GLY-PRO.itp -water tip3p -ignh -ter
>Choose CHARMM36 all-atom force field (November 2016), NH2 and COOH
>terminals
>2. gmx editconf -f ALA-GLY-GLY-PRO.gro -o ALA-GLY-GLY-PRO-box.gro -c -d
>0.8 -bt dodecahedron
>3. gmx solvate -cp ALA-GLY-GLY-PRO-box.gro -cs spc216.gro -o
>ALA-GLY-GLY-PRO-solvated.gro -p ALA-GLY-GLY-PRO.top
>4. gmx grompp -f ions.mdp -c ALA-GLY-GLY-PRO-solvated.gro -p
>ALA-GLY-GLY-PRO.top -o ions.tpr
>
> Fatal error in grompp -
>
>
> ERROR 1 [file ALA-GLY-GLY-PRO.top, line 293]:
>   No default U-B types
>
> ERROR 2 [file ALA-GLY-GLY-PRO.top, line 367]:
>   No default Proper Dih. types
>
> Meanwhile in the topology file -
>
> [ angles ]
>
>303840 5  ( line 293 )
>
>
> [ dihedral ]
>
>27263038 9  ( line 367 )
>
> ; residue   5 PRO rtp PRO  q  0.0
> 26  N  5PRO  N 26  -0.29 14.007   ;
> qtot -0.29
> 27CP3  5PRO CD 27  0 12.011   ;
> qtot -0.29
> 28HA2  5PROHD1 28   0.09  1.008   ;
> qtot -0.2
> 29HA2  5PROHD2 29   0.09  1.008   ;
> qtot -0.11
> 30CP1  5PRO CA 30   0.02 12.011   ;
> qtot -0.09
> 31HB1  5PRO HA 31   0.09  1.008   ;
> qtot 0
> 32CP2  5PRO CB 32  -0.18 12.011   ;
> qtot -0.18
> 33HA2  5PROHB1 33   0.09  1.008   ;
> qtot -0.09
> 34HA2  5PROHB2 34   0.09  1.008   ;
> qtot 0
> 35CP2  5PRO CG 35  -0.18 12.011   ;
> qtot -0.18
> 36HA2  5PROHG1 36   0.09  1.008   ;
> qtot -0.09
> 37HA2  5PROHG2 37   0.09  1.008   ;
> qtot 0
> 38 CD  5PRO  C 38   0.72 12.011   ;
> qtot 0.72
> 39 OB  5PROOT1 39  -0.5515.9994   ;
> qtot 0.17
> 40OH1  5PROOT2 40  -0.6115.9994   ;
> qtot -0.44
> 41  H  5PROHT2 41   0.44  1.008   ;
> qtot 0
>
>
> I further check if angle type between CP1, CD and OH1 exists in ffbond.itp.
> Indeed there is no such angle.  Maybe there is something wrong when using
> NH2 and COOH terminals?
>
> Please feel free to give any suggestion. I appreciate any comment.
>
> Regards,
> Simon
> --
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Re: [gmx-users] Gromacs 2016.4 - the Intel compiler and 'make check'

[Mark Abraham]

Hi,

Thanks for the report - we should look into that combination. It's highly
likely that there's some minor issue that different optimization capability
is creating or exposing. The functionality covered by that test is only
used for a few analysis tools, and the fact that gcc passes fine suggests
you should be confident in the code and icc.

Mark

On Thu, 26 Oct 2017 13:56 Mark Dixon  wrote:

> Hi there,
>
> Is there a recommended compiler for GROMACS, please?
>
> I'm trying to validate my install on a CentOS 7.4 Intel Broadwell system
> by running the tests shipped in the GROMACS source tar ball (and the
> separate regression tests).
>
> If I use GCC (4.8.5 or 7.2.0), everything passes but, if I use the Intel
> compilers (tested 16.0.2 and 17.0.1), it keeps failing on
> CorrelationsTest. I've tried pruning it down to the minimum build:
>
>cmake ../gromacs-2016.4 -DGMX_BUILD_OWN_FFTW=ON
>make -j12
>make check
>
> And I see the following:
>
> 16/27 Test #16: CorrelationsTest .***Exception: Numerical
> 0.25 sec
> [==] Running 20 tests from 2 test cases.
> [--] Global test environment set-up.
> [--] 10 tests from AutocorrTest
> [ RUN  ] AutocorrTest.EacNormal
> [   OK ] AutocorrTest.EacNormal (39 ms)
> [ RUN  ] AutocorrTest.EacNoNormalize
> [   OK ] AutocorrTest.EacNoNormalize (73 ms)
> [ RUN  ] AutocorrTest.EacCos
> [   OK ] AutocorrTest.EacCos (53 ms)
> [ RUN  ] AutocorrTest.EacVector
> [   OK ] AutocorrTest.EacVector (66 ms)
> [ RUN  ] AutocorrTest.EacRcross
>
> I delved into the build directory, hoping to find a log with a bit more
> information and found the string 'Floating point exception', but nothing
> more.
>
> Any advice you can give would be appreciated!
>
> Thanks,
>
> Mark
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Restraining one water molecule - settles vs constraints

[Hermann, Johannes]

Hi Justin,

yes everything is clear in the manual.

What I now get are lincs warnings for the OW-HW1 and OW-HW2 bond:

(exemplary for the OW-HW1 bond):

LINCS WARNING in simulation 1
relative constraint deviation after LINCS:
rms 0.317574, max 0.547778 (between atoms 1 and 2)
bonds that rotated more than 30 degrees:

Corresponding lincs parameters in the mdp file:

; options for bonds
constraints  = h-bonds
constraint-algorithm = lincs
lincs-order  = 4

Do I have to change anything else in the itp file for my "special" water 
(which I generated from tip3p.itp)? Currently I only changed the [ 
settles ] - section into the [ constraints ] section.


Thanks in advance!

Johannes

On 26.10.2017 15:25, Justin Lemkul wrote:



On 10/26/17 9:19 AM, Hermann, Johannes wrote:

Hi Justin,

thanks for the quick response! Ahhh! I looked into the manual for [ 
settles ] and  "i j   funct   length" is kind of misleading.


So this should work, right?

[ constraints ]
; i   j funct   length
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139



Yes. For reference, the contents of SETTLE are described in full in 
manual section 5.6, hopefully nothing is misleading there.


-Justin



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] No default Proper Dih. types when using neutral terminal

[Simon Kit Sang Chu]

Hi everyone,

Last time, I mentioned missing parameter for neutral terminal dihedral and
U-B type. After some debugging, I am still not sure what the cause was. I
hope providing more information could help to resolve the issue. I am using
CHARMM36 forcefield.

Brief summary of the problem -
No dihed. parameter / U-B types after using neutral terminals

Command I ran -

   1. gmx pdb2gmx -f ALA-GLY-GLY-PRO. pdb -o ALA-GLY-GLY-PRO.gro -p
   ALA-GLY-GLY-PRO.top -i ALA-GLY-GLY-PRO.itp -water tip3p -ignh -ter
   Choose CHARMM36 all-atom force field (November 2016), NH2 and COOH
   terminals
   2. gmx editconf -f ALA-GLY-GLY-PRO.gro -o ALA-GLY-GLY-PRO-box.gro -c -d
   0.8 -bt dodecahedron
   3. gmx solvate -cp ALA-GLY-GLY-PRO-box.gro -cs spc216.gro -o
   ALA-GLY-GLY-PRO-solvated.gro -p ALA-GLY-GLY-PRO.top
   4. gmx grompp -f ions.mdp -c ALA-GLY-GLY-PRO-solvated.gro -p
   ALA-GLY-GLY-PRO.top -o ions.tpr

Fatal error in grompp -


ERROR 1 [file ALA-GLY-GLY-PRO.top, line 293]:
  No default U-B types

ERROR 2 [file ALA-GLY-GLY-PRO.top, line 367]:
  No default Proper Dih. types

Meanwhile in the topology file -

[ angles ]

   303840 5  ( line 293 )


[ dihedral ]

   27263038 9  ( line 367 )

; residue   5 PRO rtp PRO  q  0.0
26  N  5PRO  N 26  -0.29 14.007   ;
qtot -0.29
27CP3  5PRO CD 27  0 12.011   ;
qtot -0.29
28HA2  5PROHD1 28   0.09  1.008   ;
qtot -0.2
29HA2  5PROHD2 29   0.09  1.008   ;
qtot -0.11
30CP1  5PRO CA 30   0.02 12.011   ;
qtot -0.09
31HB1  5PRO HA 31   0.09  1.008   ;
qtot 0
32CP2  5PRO CB 32  -0.18 12.011   ;
qtot -0.18
33HA2  5PROHB1 33   0.09  1.008   ;
qtot -0.09
34HA2  5PROHB2 34   0.09  1.008   ;
qtot 0
35CP2  5PRO CG 35  -0.18 12.011   ;
qtot -0.18
36HA2  5PROHG1 36   0.09  1.008   ;
qtot -0.09
37HA2  5PROHG2 37   0.09  1.008   ;
qtot 0
38 CD  5PRO  C 38   0.72 12.011   ;
qtot 0.72
39 OB  5PROOT1 39  -0.5515.9994   ;
qtot 0.17
40OH1  5PROOT2 40  -0.6115.9994   ;
qtot -0.44
41  H  5PROHT2 41   0.44  1.008   ;
qtot 0


I further check if angle type between CP1, CD and OH1 exists in ffbond.itp.
Indeed there is no such angle.  Maybe there is something wrong when using
NH2 and COOH terminals?

Please feel free to give any suggestion. I appreciate any comment.

Regards,
Simon
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Re: [gmx-users] Restraining one water molecule - settles vs constraints

[Justin Lemkul]

On 10/26/17 9:19 AM, Hermann, Johannes wrote:

Hi Justin,

thanks for the quick response! Ahhh! I looked into the manual for [ 
settles ] and  "i j   funct   length" is kind of misleading.


So this should work, right?

[ constraints ]
; i   j funct   length
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139



Yes. For reference, the contents of SETTLE are described in full in 
manual section 5.6, hopefully nothing is misleading there.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Restraining one water molecule - settles vs constraints

[Hermann, Johannes]

Hi Justin,

thanks for the quick response! Ahhh! I looked into the manual for [ 
settles ] and  "i j   funct   length" is kind of misleading.


So this should work, right?

[ constraints ]
; i   j funct   length
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139

Thanks, Justin!

All the best

Johannes


On 26.10.2017 15:00, Justin Lemkul wrote:



On 10/26/17 8:58 AM, Hermann, Johannes wrote:

Dear Gromacs Users, dear Justin,

I am using the tip3p water model and I want to restrain one single 
water molecule. I found Justins reply in the mailing list a few years 
ago:


/If you want to restrain a single water molecule, it needs to be 
defined as />>/its own [moleculetype] or as a part of the protein 
[moleculetype]. 
Breaking />>/apart a continuous block of water causes problems with 
the SETTLE />>/algorithm, so you will need to manually specify three 
constraints (OW-HW1, />>/OW-HW2, and HW1-HW2) for this water 
molecule, while the remaining bath of />>/solvent would be handled by 
SETTLE. />>//>>/-Justin /


I looked up in the manual how the constraints-section is formated, 
but I have no glue about the funct type. Perhaps funct 1? For the 
lengths of OW-HW1 and OW-HW2 I would assume that I take the 
bond-lengths specified in tip3p.itp, but I have no idea about the 
HW1-HW2 length.




You can find it in the SETTLE information in tip3p.itp:

[ settles ]
; i j   funct   length
1   1   0.09572 0.15139

-Justin


[ constraints ]
; i   j funct   length
1 2  1  0.09572
1 3  1  0.09572
2 3  1  ??

Can anyone help me?

Thank you very much!

All the best
Johannes





--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] Restraining one water molecule - settles vs constraints

[Justin Lemkul]

On 10/26/17 8:58 AM, Hermann, Johannes wrote:

Dear Gromacs Users, dear Justin,

I am using the tip3p water model and I want to restrain one single 
water molecule. I found Justins reply in the mailing list a few years 
ago:


/If you want to restrain a single water molecule, it needs to be 
defined as />>/its own [moleculetype] or as a part of the protein 
[moleculetype]. 
Breaking />>/apart a continuous block of water causes problems with 
the SETTLE />>/algorithm, so you will need to manually specify three 
constraints (OW-HW1, />>/OW-HW2, and HW1-HW2) for this water molecule, 
while the remaining bath of />>/solvent would be handled by SETTLE. 
/>>//>>/-Justin /


I looked up in the manual how the constraints-section is formated, but 
I have no glue about the funct type. Perhaps funct 1? For the lengths 
of OW-HW1 and OW-HW2 I would assume that I take the bond-lengths 
specified in tip3p.itp, but I have no idea about the HW1-HW2 length.




You can find it in the SETTLE information in tip3p.itp:

[ settles ]
; i j   funct   length
1   1   0.09572 0.15139

-Justin


[ constraints ]
; i   j funct   length
1 2  1  0.09572
1 3  1  0.09572
2 3  1  ??

Can anyone help me?

Thank you very much!

All the best
Johannes



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Restraining one water molecule - settles vs constraints

[Hermann, Johannes]

Dear Gromacs Users, dear Justin,

I am using the tip3p water model and I want to restrain one single water 
molecule. I found Justins reply in the mailing list a few years ago:


/If you want to restrain a single water molecule, it needs to be defined as />>/its own [moleculetype] or as a part of the protein [moleculetype]. 

Breaking />>/apart a continuous block of water causes problems with the SETTLE />>/algorithm, so you 
will need to manually specify three constraints (OW-HW1, />>/OW-HW2, and HW1-HW2) for this water molecule, 
while the remaining bath of />>/solvent would be handled by SETTLE. />>//>>/-Justin /

I looked up in the manual how the constraints-section is formated, but I 
have no glue about the funct type. Perhaps funct 1? For the lengths of 
OW-HW1 and OW-HW2 I would assume that I take the bond-lengths specified 
in tip3p.itp, but I have no idea about the HW1-HW2 length.


[ constraints ]
; i   j funct   length
1 2  1  0.09572
1 3  1  0.09572
2 3  1  ??

Can anyone help me?

Thank you very much!

All the best
Johannes

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[gmx-users] orientation of a cubic system

[GIANMARCO BARTALINI]

Hello, I have a gro file that contains a cubic system
(water+membrane+protein). Is there a way to align the box with the three
principal axes x y z? I see that with editconf -princ I can align it to x,
but y and z are pointing towards the corner of the box instead of being
aligned with the respective dimensions. I also know that I can rotate the
box setting an angle, but I would really need to find a way to do it
automatically, since I have to repeat the procedure on many different
systems. Any idea? Thank you in advance,
Gianmarco
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Re: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Elisa Pieri]

Damn, you're absolutely right..Thank you very very much! Now it is working.
We were using something done by others many years ago, we believed it was
fine (big mistake).

Thank you again!

On Thu, Oct 26, 2017 at 1:07 PM, Justin Lemkul  wrote:

>
>
> On 10/26/17 7:05 AM, Elisa Pieri wrote:
>
>> Thank you very much for the answers! We made the modifications you
>> suggested and now the error changed.
>>
>> Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
>> is linked to a retinal moiety; for this, we created a "new" residue called
>> "RET" which includes LYS+retinal. But now, Gromacs is seeing the ALA as a
>> terminal residue and is adding an oxygen, witouh making the the link
>> between ALA and RET. I suppose we have to add some parameters, but we
>> couldn't really figure out which ones. Could you help us?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_
> Residue_to_a_Force_Field#Adding_a_new_residue
>
> Sounds like you forgot step 5.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

[Justin Lemkul]

On 10/26/17 1:56 AM, Hoa Trinh wrote:

Hi all,
I am trying to look into the source code of Gromacs 5.0.7 to see how
Gromacs calculate bonded interactions. For example, to calculate bond
interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
real bonds(int nbonds, ...)
{
   
   for (i = 0; (i < nbonds); )
 {
 type = forceatoms[i++];
 ai   = forceatoms[i++];
 aj   = forceatoms[i++];

}
Is "nbonds" the total number of bond interactions? In my topology file, I
have 126 pairs in the [ bonds ] section. However, when I printf the
variable nbonds, it appears to be 378. I have no idea why. Can anyone
please help me to explain what is nbonds?


378 = 126 * 3

nbonds here indicates the size of the array, which holds (type, ai, aj) 
for each bond in the system.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Running MD simulation with Multiple ligands

[Justin Lemkul]

On 10/26/17 2:08 AM, Chamikara Herath wrote:

I need to run a MD simulation with two ligands

01. Natural Substrate (GTP)
02. Allosteric drug candidate bounds closer to the substrate binding pocket.

single itp file was created , combining both ligands using Swiss pharm for
CHARMM force field.

I am unable to continue from the add ion step because the following error
message always happens when grompp is tried to run







*Fatal error:Syntax error - File gtp_bergenin.itp, line 7Last line read:'[
atomtypes ] 'Invalid order for directive atomtypes*
I am following the following tutorial
GROMACS TutorialProtein-Ligand Complex

*Justin Lemkul*
*Department of Biochemistry, Virginia Tech*



*please kindly advice me on come across this error. *


http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Drude format file

[Justin Lemkul]

On 10/26/17 3:20 AM, limingru wrote:

Hi gmx users or developers, I am trying to do some Drude 
polarizable simulations using GMX. How to convert coordinate file (e.g pdb) 
into Drude format file? Thanks in advance.


There is no special "Drude format" for coordinate files. If you're 
referring to building on Drudes and lone pairs, pdb2gmx does all of that 
for you.


-Justin

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Justin Lemkul]

On 10/26/17 7:05 AM, Elisa Pieri wrote:

Thank you very much for the answers! We made the modifications you
suggested and now the error changed.

Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
is linked to a retinal moiety; for this, we created a "new" residue called
"RET" which includes LYS+retinal. But now, Gromacs is seeing the ALA as a
terminal residue and is adding an oxygen, witouh making the the link
between ALA and RET. I suppose we have to add some parameters, but we
couldn't really figure out which ones. Could you help us?


http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

Sounds like you forgot step 5.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Elisa Pieri]

Thank you very much for the answers! We made the modifications you
suggested and now the error changed.

Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
is linked to a retinal moiety; for this, we created a "new" residue called
"RET" which includes LYS+retinal. But now, Gromacs is seeing the ALA as a
terminal residue and is adding an oxygen, witouh making the the link
between ALA and RET. I suppose we have to add some parameters, but we
couldn't really figure out which ones. Could you help us?

Elisa

On Thu, Oct 26, 2017 at 12:01 PM, Piggot T.  wrote:

> In the line you have added into the ffnonbonded.itp it looks like the
> numbers for the LJ parameters have a comma rather than a point. So
> 2,47135e-01 rather than 2.47135e-01. I imagine this is causing the too few
> parameters on line warning
>
> Cheers
>
> Tom
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Elisa
> Pieri [elisa.pi...@univ-amu.fr]
> Sent: 26 October 2017 10:53
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic
>
> Hello again,
>
> we are trying to add Amber lipids to the Amber94 force field (actually, it
> is a version where a few years ago we added a ligand). We used pdb2gmx as
> "pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
> file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
> used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
> we got many warnings of the type
>
> This is an example of the warnings:
> WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
> (source file /home/people/Downloads/gromacs-5.1.4/src/gromacs/
> gmxpreprocess/toppush.c,
> line 338)
>
> And a fatal error:
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
> line: 742
> Fatal error: Unknown bond_atomtype hE
>
> I'm showing you what additions we made (in particular, for hE).
> We added the new atomtypes (20) in the atomtypes.atp file in the form:
> hE 1.00800  ; lipid H bonded to aliphatic carbon with 1
> electron withdrawing group
>
> Then we added the parameters in the ffbonded.itp file; example of
> stretching, bendind and torsions for hE:
>
> cA hE 10.10930   281081.1 ; lipid
>
> cA cA hE 1   110.070387.940
> cB cA hE 1   110.460393.547
> hE cA hE 1   109.550327.858
> hE cA nN 1   109.500416.559
> hE cA oH 1   109.880426.517
> hE cA oS 1   108.820425.429
> hE cA oT 1   109.500418.400
>
> cA  cA  cA  hE9   0.0  0.65103 3
> cB  cB  cA  hE9   0.0  0.0 2
> cC  cA  cA  hE9   0.0  0.65103 3
> cC  nN  cA  hE9   0.0  0.0 2
> cC  oS  cA  hE9   0.0  1.60373 3
> hA  cA  cA  hE9   0.0  0.65103 3
> hB  cB  cA  hE9   0.0  0.0 2
> hE  cA  cA  hE9   0.0  0.65103 3
> hE  cA  cA  hX9   0.0  0.65103 3
> hE  cA  cA  nA9   0.0  0.65103 3
> hE  cA  cA  nN9   0.0  0.65084 3
> hE  cA  cA  oH9   0.0  0.0 3
> hE  cA  cA  oH9   0.0  1.04600 1
> hE  cA  cA  oS9   0.0  0.0 3
> hE  cA  cA  oS9   0.0  1.04600 1
> hE  cA  cA  oT9   0.0  0.0 3
> hE  cA  cA  oT9   0.0  1.04600 1
> hE  cA  nN  hN9   0.0  0.0 2
> hE  cA  oH  hO9   0.0  2.09200 3
> hE  cA  oT  pA9   0.0  1.60387 3
>
> Same thing for the ffnonbonded.itp:
> hE   1   1.008   0.  A   2,47135e-01  6,56888e-02
>
> And then we created a lipids.rtp file (here an example for a PC part of a
> lipid):
> [ PC ]
>  [ atoms ]
>C11cC   0.798859  1
>O12oC  -0.627537  2
>O11oS  -0.424905  3
>C1 cA  -0.002091  4
>HR hE   0.119283  5
>HS hE   0.119283  6
>C2 cA   0.081076  7
>HX hE   0.131246  8
>C3 cA   0.095565  9
>HA hE   0.069089 10
>HB hE   0.069089 11
>O31oZ  -0.445682 12
>P31pA   1.076564 13
>O32oZ  -0.445682 14
>C31cA   0.363063 15
>H1AhE   0.013458 16
>H1BhE   0.013458 17
>C32cA  -0.282326 18
>H2AhX   0.164858 19
>H2B   

Re: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Piggot T .]

In the line you have added into the ffnonbonded.itp it looks like the numbers 
for the LJ parameters have a comma rather than a point. So 2,47135e-01 rather 
than 2.47135e-01. I imagine this is causing the too few parameters on line 
warning

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Elisa Pieri 
[elisa.pi...@univ-amu.fr]
Sent: 26 October 2017 10:53
To: gmx-us...@gromacs.org
Subject: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

Hello again,

we are trying to add Amber lipids to the Amber94 force field (actually, it
is a version where a few years ago we added a ligand). We used pdb2gmx as
"pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
we got many warnings of the type

This is an example of the warnings:
WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
(source file 
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line 338)

And a fatal error:
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742
Fatal error: Unknown bond_atomtype hE

I'm showing you what additions we made (in particular, for hE).
We added the new atomtypes (20) in the atomtypes.atp file in the form:
hE 1.00800  ; lipid H bonded to aliphatic carbon with 1
electron withdrawing group

Then we added the parameters in the ffbonded.itp file; example of
stretching, bendind and torsions for hE:

cA hE 10.10930   281081.1 ; lipid

cA cA hE 1   110.070387.940
cB cA hE 1   110.460393.547
hE cA hE 1   109.550327.858
hE cA nN 1   109.500416.559
hE cA oH 1   109.880426.517
hE cA oS 1   108.820425.429
hE cA oT 1   109.500418.400

cA  cA  cA  hE9   0.0  0.65103 3
cB  cB  cA  hE9   0.0  0.0 2
cC  cA  cA  hE9   0.0  0.65103 3
cC  nN  cA  hE9   0.0  0.0 2
cC  oS  cA  hE9   0.0  1.60373 3
hA  cA  cA  hE9   0.0  0.65103 3
hB  cB  cA  hE9   0.0  0.0 2
hE  cA  cA  hE9   0.0  0.65103 3
hE  cA  cA  hX9   0.0  0.65103 3
hE  cA  cA  nA9   0.0  0.65103 3
hE  cA  cA  nN9   0.0  0.65084 3
hE  cA  cA  oH9   0.0  0.0 3
hE  cA  cA  oH9   0.0  1.04600 1
hE  cA  cA  oS9   0.0  0.0 3
hE  cA  cA  oS9   0.0  1.04600 1
hE  cA  cA  oT9   0.0  0.0 3
hE  cA  cA  oT9   0.0  1.04600 1
hE  cA  nN  hN9   0.0  0.0 2
hE  cA  oH  hO9   0.0  2.09200 3
hE  cA  oT  pA9   0.0  1.60387 3

Same thing for the ffnonbonded.itp:
hE   1   1.008   0.  A   2,47135e-01  6,56888e-02

And then we created a lipids.rtp file (here an example for a PC part of a
lipid):
[ PC ]
 [ atoms ]
   C11cC   0.798859  1
   O12oC  -0.627537  2
   O11oS  -0.424905  3
   C1 cA  -0.002091  4
   HR hE   0.119283  5
   HS hE   0.119283  6
   C2 cA   0.081076  7
   HX hE   0.131246  8
   C3 cA   0.095565  9
   HA hE   0.069089 10
   HB hE   0.069089 11
   O31oZ  -0.445682 12
   P31pA   1.076564 13
   O32oZ  -0.445682 14
   C31cA   0.363063 15
   H1AhE   0.013458 16
   H1BhE   0.013458 17
   C32cA  -0.282326 18
   H2AhX   0.164858 19
   H2BhX   0.164858 20
   N31nA   0.198554 21
   C33cA  -0.395982 22
   H3AhX   0.194775 23
   H3BhX   0.194775 24
   H3ChX   0.194775 25
   C34cA  -0.395982 26
   H4AhX   0.194775 27
   H4BhX   0.194775 28
   H4ChX   0.194775 29
   C35cA  -0.395982 30
   H5AhX   0.194775 31
   H5BhX   0.194775 32
   H5ChX   0.194775 33
   O33oP  -0.793092 34
   O34oP  -0.793092 35
   O21oS  -0.390929 36
   C21

Re: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Mark Abraham]

Hi,

I don't recall whether lower case is supported here, I imagine it might not
be because historically FORTRAN-era force fields used all caps. You could
try using only upper case.

Mark

On Thu, Oct 26, 2017 at 11:53 AM Elisa Pieri 
wrote:

> Hello again,
>
> we are trying to add Amber lipids to the Amber94 force field (actually, it
> is a version where a few years ago we added a ligand). We used pdb2gmx as
> "pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
> file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
> used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
> we got many warnings of the type
>
> This is an example of the warnings:
> WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
> (source file
> /home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
> line 338)
>
> And a fatal error:
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
> line: 742
> Fatal error: Unknown bond_atomtype hE
>
> I'm showing you what additions we made (in particular, for hE).
> We added the new atomtypes (20) in the atomtypes.atp file in the form:
> hE 1.00800  ; lipid H bonded to aliphatic carbon with 1
> electron withdrawing group
>
> Then we added the parameters in the ffbonded.itp file; example of
> stretching, bendind and torsions for hE:
>
> cA hE 10.10930   281081.1 ; lipid
>
> cA cA hE 1   110.070387.940
> cB cA hE 1   110.460393.547
> hE cA hE 1   109.550327.858
> hE cA nN 1   109.500416.559
> hE cA oH 1   109.880426.517
> hE cA oS 1   108.820425.429
> hE cA oT 1   109.500418.400
>
> cA  cA  cA  hE9   0.0  0.65103 3
> cB  cB  cA  hE9   0.0  0.0 2
> cC  cA  cA  hE9   0.0  0.65103 3
> cC  nN  cA  hE9   0.0  0.0 2
> cC  oS  cA  hE9   0.0  1.60373 3
> hA  cA  cA  hE9   0.0  0.65103 3
> hB  cB  cA  hE9   0.0  0.0 2
> hE  cA  cA  hE9   0.0  0.65103 3
> hE  cA  cA  hX9   0.0  0.65103 3
> hE  cA  cA  nA9   0.0  0.65103 3
> hE  cA  cA  nN9   0.0  0.65084 3
> hE  cA  cA  oH9   0.0  0.0 3
> hE  cA  cA  oH9   0.0  1.04600 1
> hE  cA  cA  oS9   0.0  0.0 3
> hE  cA  cA  oS9   0.0  1.04600 1
> hE  cA  cA  oT9   0.0  0.0 3
> hE  cA  cA  oT9   0.0  1.04600 1
> hE  cA  nN  hN9   0.0  0.0 2
> hE  cA  oH  hO9   0.0  2.09200 3
> hE  cA  oT  pA9   0.0  1.60387 3
>
> Same thing for the ffnonbonded.itp:
> hE   1   1.008   0.  A   2,47135e-01  6,56888e-02
>
> And then we created a lipids.rtp file (here an example for a PC part of a
> lipid):
> [ PC ]
>  [ atoms ]
>C11cC   0.798859  1
>O12oC  -0.627537  2
>O11oS  -0.424905  3
>C1 cA  -0.002091  4
>HR hE   0.119283  5
>HS hE   0.119283  6
>C2 cA   0.081076  7
>HX hE   0.131246  8
>C3 cA   0.095565  9
>HA hE   0.069089 10
>HB hE   0.069089 11
>O31oZ  -0.445682 12
>P31pA   1.076564 13
>O32oZ  -0.445682 14
>C31cA   0.363063 15
>H1AhE   0.013458 16
>H1BhE   0.013458 17
>C32cA  -0.282326 18
>H2AhX   0.164858 19
>H2BhX   0.164858 20
>N31nA   0.198554 21
>C33cA  -0.395982 22
>H3AhX   0.194775 23
>H3BhX   0.194775 24
>H3ChX   0.194775 25
>C34cA  -0.395982 26
>H4AhX   0.194775 27
>H4BhX   0.194775 28
>H4ChX   0.194775 29
>C35cA  -0.395982 30
>H5AhX   0.194775 31
>H5BhX   0.194775 32
>H5ChX   0.194775 33
>O33oP  -0.793092 34
>O34oP  -0.793092 35
>O21oS  -0.390929 36
>C21cC   0.787558 37
>O22oC  -0.625551 38
>  [ bonds ]
> C11   O12
> 

[gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Elisa Pieri]

Hello again,

we are trying to add Amber lipids to the Amber94 force field (actually, it
is a version where a few years ago we added a ligand). We used pdb2gmx as
"pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
we got many warnings of the type

This is an example of the warnings:
WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
(source file 
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line 338)

And a fatal error:
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742
Fatal error: Unknown bond_atomtype hE

I'm showing you what additions we made (in particular, for hE).
We added the new atomtypes (20) in the atomtypes.atp file in the form:
hE 1.00800  ; lipid H bonded to aliphatic carbon with 1
electron withdrawing group

Then we added the parameters in the ffbonded.itp file; example of
stretching, bendind and torsions for hE:

cA hE 10.10930   281081.1 ; lipid

cA cA hE 1   110.070387.940
cB cA hE 1   110.460393.547
hE cA hE 1   109.550327.858
hE cA nN 1   109.500416.559
hE cA oH 1   109.880426.517
hE cA oS 1   108.820425.429
hE cA oT 1   109.500418.400

cA  cA  cA  hE9   0.0  0.65103 3
cB  cB  cA  hE9   0.0  0.0 2
cC  cA  cA  hE9   0.0  0.65103 3
cC  nN  cA  hE9   0.0  0.0 2
cC  oS  cA  hE9   0.0  1.60373 3
hA  cA  cA  hE9   0.0  0.65103 3
hB  cB  cA  hE9   0.0  0.0 2
hE  cA  cA  hE9   0.0  0.65103 3
hE  cA  cA  hX9   0.0  0.65103 3
hE  cA  cA  nA9   0.0  0.65103 3
hE  cA  cA  nN9   0.0  0.65084 3
hE  cA  cA  oH9   0.0  0.0 3
hE  cA  cA  oH9   0.0  1.04600 1
hE  cA  cA  oS9   0.0  0.0 3
hE  cA  cA  oS9   0.0  1.04600 1
hE  cA  cA  oT9   0.0  0.0 3
hE  cA  cA  oT9   0.0  1.04600 1
hE  cA  nN  hN9   0.0  0.0 2
hE  cA  oH  hO9   0.0  2.09200 3
hE  cA  oT  pA9   0.0  1.60387 3

Same thing for the ffnonbonded.itp:
hE   1   1.008   0.  A   2,47135e-01  6,56888e-02

And then we created a lipids.rtp file (here an example for a PC part of a
lipid):
[ PC ]
 [ atoms ]
   C11cC   0.798859  1
   O12oC  -0.627537  2
   O11oS  -0.424905  3
   C1 cA  -0.002091  4
   HR hE   0.119283  5
   HS hE   0.119283  6
   C2 cA   0.081076  7
   HX hE   0.131246  8
   C3 cA   0.095565  9
   HA hE   0.069089 10
   HB hE   0.069089 11
   O31oZ  -0.445682 12
   P31pA   1.076564 13
   O32oZ  -0.445682 14
   C31cA   0.363063 15
   H1AhE   0.013458 16
   H1BhE   0.013458 17
   C32cA  -0.282326 18
   H2AhX   0.164858 19
   H2BhX   0.164858 20
   N31nA   0.198554 21
   C33cA  -0.395982 22
   H3AhX   0.194775 23
   H3BhX   0.194775 24
   H3ChX   0.194775 25
   C34cA  -0.395982 26
   H4AhX   0.194775 27
   H4BhX   0.194775 28
   H4ChX   0.194775 29
   C35cA  -0.395982 30
   H5AhX   0.194775 31
   H5BhX   0.194775 32
   H5ChX   0.194775 33
   O33oP  -0.793092 34
   O34oP  -0.793092 35
   O21oS  -0.390929 36
   C21cC   0.787558 37
   O22oC  -0.625551 38
 [ bonds ]
C11   O12
C11   O11
O11   C1
C1HR
C1HS
C1C2
C2HX
C2C3
C2O21
C3HA
C3HB
C3O31
O31   P31
P31   O32
P31   033
P31   034
O32   C31
C31   H1A
C31   H1B
C31   C32
C32   H2A
C32   H2B
C32   N31
N31   C33
N31   C34
N31   C35
C33   H3A
C33   H3B
C33   H3C
C34   H4A
C34   H4B
C34   H4C
C35   H5A
C35   H5B
C35   H5C
O21   

[gmx-users] Drude format file

[limingru]

Hi gmx users or developers, I am trying to do some Drude 
polarizable simulations using GMX. How to convert coordinate file (e.g pdb) 
into Drude format file? Thanks in advance.



School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  





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[gmx-users] Running MD simulation with Multiple ligands

[Chamikara Herath]

I need to run a MD simulation with two ligands

01. Natural Substrate (GTP)
02. Allosteric drug candidate bounds closer to the substrate binding pocket.

single itp file was created , combining both ligands using Swiss pharm for
CHARMM force field.

I am unable to continue from the add ion step because the following error
message always happens when grompp is tried to run







*Fatal error:Syntax error - File gtp_bergenin.itp, line 7Last line read:'[
atomtypes ] 'Invalid order for directive atomtypes*
I am following the following tutorial
GROMACS TutorialProtein-Ligand Complex

*Justin Lemkul*
*Department of Biochemistry, Virginia Tech*



*please kindly advice me on come across this error. *



*I can provide topology files *
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Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

[Mark Abraham]

Hi,

It's only the number of that type of bond, and there are very many types of
bond. Note that pairs are handled in their own routine.

You should really be modifying newer versions of GROMACS. Doing so off an
old released version ensures you benefit from none of the improvements or
bug fixes since then, and makes it harder for your effort to remain
relevant in the future. And please use version control ;-)

Mark

On Thu, 26 Oct 2017 07:56 Hoa Trinh  wrote:

> Hi all,
> I am trying to look into the source code of Gromacs 5.0.7 to see how
> Gromacs calculate bonded interactions. For example, to calculate bond
> interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
> real bonds(int nbonds, ...)
> {
>   
>   for (i = 0; (i < nbonds); )
> {
> type = forceatoms[i++];
> ai   = forceatoms[i++];
> aj   = forceatoms[i++];
> 
> }
> Is "nbonds" the total number of bond interactions? In my topology file, I
> have 126 pairs in the [ bonds ] section. However, when I printf the
> variable nbonds, it appears to be 378. I have no idea why. Can anyone
> please help me to explain what is nbonds?
> Thank you very much in advance.
> Best regards,
>
> *Lan Hoa*
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