Re: [gmx-users] adding new ion within the oplsaa force field

[Jose Borreguero]

yes, the ions I have can be considered as bound. I found out I also had to
declare the type of residue as "Ion" in file residues.dat :)

On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul  wrote:

>
>
> On 6/23/17 3:50 PM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I'm trying to add a new type of atom as an ion. Looking at already
>> existing
>> ions, such as sodium (NA), I see there's an entry both in files ions.itp
>> and aminoacids.rtp. My question is, what is the rationale of declaring
>> ions
>> both as ions and as residues? Is this always required?
>>
>>
> If you want to process it with pdb2gmx, you need an entry in an .rtp
> file.  If you just have an ion that you're going to add into a box, you can
> rely on ions.itp.  The current implementation covers both cases.  Some
> structures have bound ions and it makes life easier to be able to process
> them with pdb2gmx.
>
> -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] adding new ion within the oplsaa force field

[Justin Lemkul]

On 6/23/17 3:50 PM, Jose Borreguero wrote:

Dear Gromacs users,

I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both as ions and as residues? Is this always required?



If you want to process it with pdb2gmx, you need an entry in an .rtp file.  If 
you just have an ion that you're going to add into a box, you can rely on 
ions.itp.  The current implementation covers both cases.  Some structures have 
bound ions and it makes life easier to be able to process them with pdb2gmx.


-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] adding new ion within the oplsaa force field

[Smith, Micholas D.]

If you want the ion to be recognized as an individual residue, you need to 
stick it in the *.rtp file. 

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jose 
Borreguero 
Sent: Friday, June 23, 2017 3:50 PM
To: gromacs
Subject: [gmx-users] adding new ion within the oplsaa force field

Dear Gromacs users,

I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both as ions and as residues? Is this always required?

Best,
Jose Borreguero
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[gmx-users] adding new ion within the oplsaa force field

[Jose Borreguero]

Dear Gromacs users,

I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both as ions and as residues? Is this always required?

Best,
Jose Borreguero
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Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Rana Rehan Khalid]

Dear sir i have force field for O2 now some one work over it before its the
.prm file he use to run simulation amber99 force field and use there own
lab heme generated ff heme fe 02  now how i can use these amber heme
force field in Gromacs thanks.

On Fri, Jun 16, 2017 at 3:23 AM, Mark Abraham 
wrote:

> Hi,
>
> Generating a suitable model for such a system, plus its parameters, is a
> lot of work, generally unsuitable for a beginner, and IMO unlikely to work
> well. As I have suggested before, start by reading the literature for what
> others have done. Maybe your problem is solved, maybe it should not be
> attempted. :-)
>
> Mark
>
> On Fri, 16 Jun 2017 01:39 Rana Rehan Khalid  wrote:
>
> > kindly tell me sir how i can i add residue
> >
> > On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid 
> > wrote:
> >
> > > thanks justin
> > > actually i want to know that how these values of column (atom name,
> type,
> > > charge and charge group) we obtain for oxygen bonded with heme fe. is
> > there
> > > any program through which i find the parameter file for oxygen with
> heme
> > > and nitric oxide with heme iron. if i just add the atom name type and
> > > charge in the bonded type heme fe atoms is it work for me can you tell
> me
> > > about any tutorial in which adding residue shows with examples that
> will
> > be
> > > very understandable. thanks
> > >
> > > On Wed, Jun 14, 2017 at 4:54 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:
> > >>
> > >>> Hi
> > >>> I have read the chapter 5 of manual but i am confuse how can i add
> > >>> residue
> > >>> into heme atom of .rtp ff
> > >>> this is the coordinate due to which error come
> > >>>
> > >>> HETATM 1529  O01 HEM   187   3.996  19.101  70.594  0.00
> > >>> 0.00   O
> > >>>
> > >>> kindly guide me how i can make changes in the rtp file and .atp so
> that
> > >>> this error remove
> > >>> here is the heme rtp part of my selected ff where i can add O01 and
> > also
> > >>> tell me these 4 column and these values and tell me which value i add
> > for
> > >>> O01 like (FE FE 0.4 0 )
> > >>>
> > >>
> > >> You should refer back to the manual if the contents of these files are
> > >> not clear.  You're seeking to introduce new parameters for an
> > oxygen-bound
> > >> form of heme; this may require very complex parametrization work.
> > >> Modifying an .rtp file is trivial; it's just text.  Putting realistic
> > >> parameters into it is a whole other matter.  Check the literature for
> > any
> > >> existing efforts to avoid duplicated work.
> > >>
> > >> -Justin
> > >>
> > >> [ HEME ]
> > >>>   [ atoms ]
> > >>> FEFE 0.4 0
> > >>> NANR-0.1 0
> > >>> NBNR-0.1 0
> > >>> NCNR-0.1 0
> > >>> NDNR-0.1 0
> > >>>CHA C-0.1 1
> > >>>HHAHC 0.1 1
> > >>>C1A C 0.0 2
> > >>>C2A C 0.0 2
> > >>>C3A C 0.0 2
> > >>>C4A C 0.0 2
> > >>>CMA   CH3 0.0 3
> > >>>CAA   CH2 0.0 4
> > >>>CBA   CH2 0.0 4
> > >>>CGA C 0.27000 5
> > >>>O1AOM-0.63500 5
> > >>>O2AOM-0.63500 5
> > >>>CHB C-0.1 6
> > >>>HHBHC 0.1 6
> > >>>C1B C 0.0 7
> > >>>C2B C 0.0 7
> > >>>C3B C 0.0 7
> > >>>C4B C 0.0 7
> > >>>CMB   CH3 0.0 8
> > >>>CAB   CR1 0.0 9
> > >>>CBB   CH2 0.0 9
> > >>>CHC C-0.110
> > >>>HHCHC 0.110
> > >>>C1C C 0.011
> > >>>C2C C 0.011
> > >>>C3C C 0.011
> > >>>C4C C 0.011
> > >>>CMC   CH3 0.012
> > >>>CAC   CR1 0.013
> > >>>CBC   CH2 0.013
> > >>>CHD C-0.114
> > >>>HHDHC 0.114
> > >>>C1D C 0.015
> > >>>C2D C 0.015
> > >>>C3D C 0.015
> > >>>C4D C 0.015
> > >>>CMD   CH3 0.016
> > >>>CAD   CH2 0.017
> > >>>CBD   CH2 0.017
> > >>>CGD C 0.2700018
> > >>>O1DOM-0.6350018
> > >>>O2DOM-0.6350018
> > >>>
> > >>> thanks
> > >>>
> > >>>
> > >> --
> > >> ==
> > >>
> > >> 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
> > 

Re: [gmx-users] Scaling GROMACS

[Mark Abraham]

Hi,

Once you've compiled GROMACS for this machine (will run at least twice as
fast), your setup is likely optimal. The options and what to do with them
are all in the 5.1 gromacs user guide online.

Mark

On Fri, 23 Jun 2017 16:10 Sergio Manzetti 
wrote:

> Hi, I have the following system:
>
> Running on 1 node with total 24 cores, 24 logical cores
> Hardware detected:
> CPU info:
> Vendor: AuthenticAMD
> Brand: AMD Opteron(tm) Processor 6344
> SIMD instructions most likely to fit this hardware: AVX_128_FMA
> SIMD instructions selected at GROMACS compile time: SSE2
>
> Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this
> machine, which is better
>
> Reading file topol.tpr, VERSION 5.1.2 (single precision)
> Using 12 MPI threads
> Using 1 OpenMP thread per tMPI thread
>
>
> When running 4 separate jobs, does gcom -1 or other options in mdrun help
> in subdividing the tasks?
>
>
> Sergio
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
> --
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Re: [gmx-users] CGMD with cut-off Verlet?

[Mark Abraham]

Hi,

And follow the advice of the Martini authors for using the Verlet scheme
with their forcefield.

Mark

On Fri, 23 Jun 2017 17:20 Justin Lemkul  wrote:

>
>
> On 6/23/17 11:08 AM, Alex Mathew wrote:
> > Dear all,
> >
> > While running CGMD in GPU i got this error
> >
> > OpenMP threads have been requested with cut-off scheme Group, but these
> are
> > only supported with cut-off scheme Verlet
> >
> > Here can i change the cut-off scheme to Verlet ?
>
> Amazingly enough:
>
> cutoff-scheme = Verlet
>
> in the .mdp file :)
>
> -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] Constraint vs. Umbrella in Pull COM

[Angela Marcela Murcia Rios]

Thank you for the clarification!


-Angela



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

Sent: June 22, 2017 7:57 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Constraint vs. Umbrella in Pull COM

In the case of SHAKE constraint, there is no spring-like physics, like in
umbrella pulling. The distance between COMs evolves according to the rate
you set, but there is no COM oscillation around prescribed values, SHAKE
turns the distance into a solid stick.

Alex

On Thu, Jun 22, 2017 at 5:13 PM, Angela Marcela Murcia Rios  wrote:

> Hi All,
>
>
> I was wondering if someone knows the difference between constraint versus
> umbrella pulling. I have read the manual but I'm still not sure what this
> means.
>
>
> 1. Umbrella pulling: A harmonic potential is applied between the centers
> of mass of two groups. Thus, the force is proportional to the displacement.
> 2. Constraint pulling: The distance between the centers of mass of two
> groups is constrained. The constraint force can be written to a file. This
> method uses the SHAKE algorithm but only needs 1 iteration to be exact if
> only two groups are constrained.
>
> What does it mean by "The distance between the centers of mass of two
> groups is constrained"? Is this distance fixed? or is the reference group
> assumed to be fixed?
>
> Thanks for the help!
>
> -Angela
>
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Re: [gmx-users] Scaling GROMACS

[Justin Lemkul]

On 6/23/17 10:04 AM, Sergio Manzetti wrote:

Hi, I have the following system:

Running on 1 node with total 24 cores, 24 logical cores
Hardware detected:
CPU info:
Vendor: AuthenticAMD
Brand: AMD Opteron(tm) Processor 6344
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this 
machine, which is better



Make sure to re-compile properly to get good performance.


Reading file topol.tpr, VERSION 5.1.2 (single precision)
Using 12 MPI threads
Using 1 OpenMP thread per tMPI thread


When running 4 separate jobs, does gcom -1 or other options in mdrun help in 
subdividing the tasks?



You can pin a job to specific cores to avoid resources fighting one another with 
-pin and -pinoffset.


-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] CG MD

[Justin Lemkul]

On 6/23/17 10:26 AM, Alex Mathew wrote:

Dear all,
I was wondering the analysis we usually use in the all-atom simulation will
work in for CG model?
I guess secondary structural analysis will be useless since it's not
considering all atoms. What about non-bonded energies and other parameters
such hydrogen bond and essential dynamics?


What do people do in the literature to address the same types of questions 
you're asking.  H-bonding is a microscopic property and likely is not going to 
be addressed via CG, though most atomistic properties can be studied by 
rebuilding the atomistic coordinates from the CG.  Various methods exist to do this.


-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] CGMD with cut-off Verlet?

[Justin Lemkul]

On 6/23/17 11:08 AM, Alex Mathew wrote:

Dear all,

While running CGMD in GPU i got this error

OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet

Here can i change the cut-off scheme to Verlet ?


Amazingly enough:

cutoff-scheme = Verlet

in the .mdp file :)

-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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[gmx-users] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?

[lan hoa Trinh]

Hi all,
I am reading the paper "Replica-exchange molecular dynamics method for
protein folding" by Yuko Okamoto. In this paper, they exchange temperatures
of 2 replica. To evaluate that replica exchange is successful, they
calculate exchange probability; plot the temperature, potential energy per
replica versue time.
In Gromacs, coordinates of replica are exchanged instead. So besides
evaluating exchange probability, how do I know that the replica exchange is
sucessful? Since we exchange coordinate, one replica just stay at 1
temperature, so we will not see the result of the paper by Yuko, I mean,
one replica actually visit all the temperature. How about potential energy,
should I expect that one replica visit all range of potential energy when
we exchange coordinates of replica?
Also, is this bad if exchange probability too high, let's say 0.8?
Thanks in advance.
Best regards,
*Lan Hoa*
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[gmx-users] CGMD with cut-off Verlet?

[Alex Mathew]

Dear all,

While running CGMD in GPU i got this error

OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet

Here can i change the cut-off scheme to Verlet ?
ff is martini22p
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[gmx-users] Legacy Test Failure with GMX 5.1.4

[Daniel Kozuch]

Hello,

I am recompiling GROMACS on a new compute node and I am getting a unit test
failure (shown below). I am compiling with GNU 4.8.5 and the following
cmake commands:
cmake .. -DCMAKE_INSTALL_PREFIX=[redacted] -DGMX_MPI=on -DGMX_GPU=off
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_THREAD_MPI=off.

I am unsure how to fix this error, does anyone have any suggestions?

Best,
Dan

 Start  1: TestUtilsUnitTests
 1/26 Test  #1: TestUtilsUnitTests ...   Passed0.57 sec
  Start  2: GmxlibTests
 2/26 Test  #2: GmxlibTests ..   Passed0.56 sec
  Start  3: MdlibUnitTest
 3/26 Test  #3: MdlibUnitTest    Passed0.56 sec
  Start  4: CommandLineUnitTests
 4/26 Test  #4: CommandLineUnitTests .   Passed0.58 sec
  Start  5: FFTUnitTests
 5/26 Test  #5: FFTUnitTests .   Passed0.63 sec
  Start  6: MathUnitTests
 6/26 Test  #6: MathUnitTests    Passed0.56 sec
  Start  7: RandomUnitTests
 7/26 Test  #7: RandomUnitTests ..   Passed0.56 sec
  Start  8: OnlineHelpUnitTests
 8/26 Test  #8: OnlineHelpUnitTests ..   Passed0.57 sec
  Start  9: OptionsUnitTests
 9/26 Test  #9: OptionsUnitTests .   Passed0.56 sec
  Start 10: UtilityUnitTests
10/26 Test #10: UtilityUnitTests .   Passed0.57 sec
  Start 11: FileIOTests
11/26 Test #11: FileIOTests ..   Passed0.56 sec
  Start 12: SimdUnitTests
12/26 Test #12: SimdUnitTests    Passed0.58 sec
  Start 13: LegacyToolsTests
13/26 Test #13: LegacyToolsTests .***Failed0.56 sec
[redacted] no hfi units are active (err=23)
[==] Running 12 tests from 2 test cases.
[--] Global test environment set-up.
[--] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
[ RUN  ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
Group 0 ( System) has 6 elements
Group 1 (  Water) has 6 elements
Group 2 (SOL) has 6 elements
Select a group:
---
Program legacy-tools-test, VERSION 5.1.4
Source code file: [redacted]/gromacs-5.1.4/src/gromacs/topology/index.cpp,
line: 917

Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Halting program legacy-tools-test
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--

  Start 14: GmxPreprocessTests
14/26 Test #14: GmxPreprocessTests ...   Passed0.66 sec
  Start 15: CorrelationsTest
15/26 Test #15: CorrelationsTest .   Passed0.84 sec
  Start 16: AnalysisDataUnitTests
16/26 Test #16: AnalysisDataUnitTests    Passed0.59 sec
  Start 17: SelectionUnitTests
17/26 Test #17: SelectionUnitTests ...   Passed0.69 sec
  Start 18: TrajectoryAnalysisUnitTests
18/26 Test #18: TrajectoryAnalysisUnitTests ..   Passed0.89 sec
  Start 19: MdrunTests
19/26 Test #19: MdrunTests ...   Passed2.10 sec
  Start 20: MdrunMpiTests
20/26 Test #20: MdrunMpiTests    Passed0.96 sec
  Start 21: regressiontests/simple
21/26 Test #21: regressiontests/simple ...   Passed   47.05 sec
  Start 22: regressiontests/complex
22/26 Test #22: regressiontests/complex ..   Passed  149.94 sec
  Start 23: regressiontests/kernel
23/26 Test #23: regressiontests/kernel ...   Passed  436.31 sec
  Start 24: regressiontests/freeenergy
24/26 Test #24: regressiontests/freeenergy ...   Passed   35.35 sec
  Start 25: regressiontests/pdb2gmx
25/26 Test #25: regressiontests/pdb2gmx ..   Passed  109.15 sec
  Start 26: regressiontests/rotation
26/26 Test #26: regressiontests/rotation .   Passed   36.78 sec

96% tests passed, 1 tests failed out of 26

Label Time Summary:
GTest =  10.52 sec
IntegrationTest   =   2.65 sec
MpiIntegrationTest=   0.96 sec
UnitTest  =  10.52 sec

Total Test time (real) = 828.73 sec

The following tests FAILED:
 13 - LegacyToolsTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest] Error 8
make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2
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[gmx-users] CG MD

[Alex Mathew]

Dear all,
I was wondering the analysis we usually use in the all-atom simulation will
work in for CG model?
I guess secondary structural analysis will be useless since it's not
considering all atoms. What about non-bonded energies and other parameters
such hydrogen bond and essential dynamics?
Thanks
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[gmx-users] Scaling GROMACS

[Sergio Manzetti]

Hi, I have the following system: 

Running on 1 node with total 24 cores, 24 logical cores 
Hardware detected: 
CPU info: 
Vendor: AuthenticAMD 
Brand: AMD Opteron(tm) Processor 6344 
SIMD instructions most likely to fit this hardware: AVX_128_FMA 
SIMD instructions selected at GROMACS compile time: SSE2 

Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this 
machine, which is better 

Reading file topol.tpr, VERSION 5.1.2 (single precision) 
Using 12 MPI threads 
Using 1 OpenMP thread per tMPI thread 


When running 4 separate jobs, does gcom -1 or other options in mdrun help in 
subdividing the tasks? 


Sergio 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
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Norge 
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 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Qing Lv]

The problem has been solved. I forgot to delete some entries when using .top 
file as .itp file.


Thanks,
Qing


At 2017-06-23 15:36:32, "Mark Abraham"  wrote:
>Hi,
>
>You can't just paste together two topology files intended to stand alone
>e.g. because they have [defaults] sections. You can #include files, but
>they have to follow the structure of the example in chapter 5 of the manual
>(and every tutorial). Defaults, then atomtypes and parameters, then
>moleculetypes, then system.
>
>Mark
>
>On Fri, Jun 23, 2017 at 5:47 AM Qing Lv  wrote:
>
>> I changed the order of .itp file and put the "topol_ATP.itp" ahead of
>> protein.itp . However, I got the following errors this time:
>> Fatal error:
>> Syntax error - File forcefield.itp, line 6
>> Last line read:
>> '  11   no  1.0 1.0'
>> Found a second defaults directive.
>>
>>
>> P.S.
>> My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+
>> (probably inappropriate) but still got the same errors.
>>
>>
>> Thanks,
>> Qing
>>
>>
>>
>> At 2017-06-23 09:46:49, "Qing Lv"  wrote:
>> >Dear All,
>> >
>> >
>> >I am setting up a simulation of protein-ATP complex. I manually combined
>> the coordinates and topologies of the protein and ATP together, and ran
>> editconf and solvate successfully. However, when I ran grompp, errors
>> occurred:
>> >Syntax error - File forcefield.itp, line 4
>> >Last line read:
>> >'[ defaults ]'
>> >Invalid order for directive defaults
>> >
>> >
>> >I checked the .itp files I used and did not find "[ defaults ]" pattern.
>> How to fix it?
>> >Thanks,
>> >Qing
>> >--
>> >Gromacs Users mailing list
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

At 2017-06-23 21:55:39, "Justin Lemkul"  wrote:
>
>
>On 6/23/17 9:53 AM, Qing Lv wrote:
>> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither 
>> work...
>
>There is no chain information in a .gro so this approach cannot work.  If you 
>have a multimeric complex, and you need to use these weird 5-character names, 
>process each .gro separately and merge the topologies manually (convert .top 
>-> 
>.itp and list them as #include statements in a new .top).



This is just what I have tried and succeeded eventually... Previously I made 
some mistakes when converting .top files to .itp.
Thanks.
Qing


>
>Or:
>
>1. Use a different force field that doesn't require format-breaking atom names.
>2. Change the names in the .rtp and coordinate file to preserve format 
>standards.
>
>-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] 5-letter atom names in topology files

[Justin Lemkul]

On 6/23/17 9:53 AM, Qing Lv wrote:

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...


There is no chain information in a .gro so this approach cannot work.  If you 
have a multimeric complex, and you need to use these weird 5-character names, 
process each .gro separately and merge the topologies manually (convert .top -> 
.itp and list them as #include statements in a new .top).


Or:

1. Use a different force field that doesn't require format-breaking atom names.
2. Change the names in the .rtp and coordinate file to preserve format 
standards.

-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] 5-letter atom names in topology files

[Qing Lv]

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
Qing


At 2017-06-23 17:19:55, "Fitsiou, Eleni"  wrote:
>Hi ,
>Rename your chains and you could use   -merge interactive and  the -ter flag
>Best 
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Re: [gmx-users] Gigantic boxes

[Sergio Manzetti]

Thanks, that fixed it! 




Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Friday, June 23, 2017 3:49:38 PM 
Subject: Re: [gmx-users] Gigantic boxes 

On 6/23/17 6:20 AM, Sergio Manzetti wrote: 
> Hi, I Have prepared a box, which just grows beyond proportions in order to 
> satisfy grompp complaining about the box being less than the double of rlist, 
> so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the 
> box quickly becomes over 14x14x14. When one visualizes it one can see that 
> the molecule is surrounded by at least 5 Å of waters in all directions, so 
> there is plenty of water in the system. Nevertheless, grompp wants even 
> bigger box, and thus more water. 
> 
> Is this common in MD simulations to run megaboxes for molecules that are 
> virtually disappearing in the large water molecule number? 
> 

No, it's not. Make sure you're specifying your cutoffs in nm, not A. 

-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] Regarding creating a itp for molecule from CGenFF

[Justin Lemkul]

On 6/23/17 1:02 AM, Dilip H N wrote:

Hello all,

I want to simulate methylamine with amino acid misture in CHARMM FF, so i
have created methylamine in mol2 format and created the .itp and .pdb files
from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
included it in topology file also as:-  #Include "methylamine.itp", have
solvated the system,
But if i give the command for energy minimization:-
gmx grompp -f em.mdp -c abc.gro -p topol.top -o em.tpr
i am getting the error as

NOTE 1 [file em.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.

Setting the LD random seed to -1252943664
Generated 85052 of the 85078 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 55198 of the 85078 1-4 parameter combinations

ERROR 1 [file Dimethylamine.itp, line 9]:
   Atomtype 7 not found

How can i solve these error..??



Integers aren't valid atom types, so something in your ligand topology is 
complete garbage.


-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] Gigantic boxes

[Justin Lemkul]

On 6/23/17 6:20 AM, Sergio Manzetti wrote:

Hi, I Have prepared a box, which just grows beyond proportions in order to 
satisfy grompp complaining about the box being less than the double of rlist, 
so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box 
quickly becomes over 14x14x14. When one visualizes it one can see that the 
molecule is surrounded by at least 5 Å of waters in all directions, so there is 
plenty of water in the system. Nevertheless, grompp wants even bigger box, and 
thus more water.

Is this common in MD simulations to run megaboxes for molecules that are 
virtually disappearing in the large water molecule number?



No, it's not.  Make sure you're specifying your cutoffs in nm, not A.

-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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[gmx-users] Box size and Force field

[Sergio Manzetti]

Hi, it seems that there is something with the force field that gives issues: 

The same parameters are used for 5 molecules in a test run: 

Using AMBER99SB ISTN : 

2 of 5 small molecules work perfectly in the simulation in water. 

3 of the 5 small molecules stop at grompp MD.mdp step giving the problem of 
rlist being too high and the box size too small. Increasing box size or 
decreasing rlist does not help. 


Nothing can be made unless changing force field, because all other options have 
been tried. 


Does anyone know an option that can solve this 
? 

Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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[gmx-users] Gigantic boxes

[Sergio Manzetti]

Hi, I Have prepared a box, which just grows beyond proportions in order to 
satisfy grompp complaining about the box being less than the double of rlist, 
so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box 
quickly becomes over 14x14x14. When one visualizes it one can see that the 
molecule is surrounded by at least 5 Å of waters in all directions, so there is 
plenty of water in the system. Nevertheless, grompp wants even bigger box, and 
thus more water. 

Is this common in MD simulations to run megaboxes for molecules that are 
virtually disappearing in the large water molecule number? 

Sergio 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] 5-letter atom names in topology files

[Fitsiou, Eleni]

Hi ,
Rename your chains and you could use   -merge interactive and  the -ter flag
Best 
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I 
used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1 
and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since 
there is no chain separators in GRO files (like "TER" in PDB), pdb2gmx might 
regard all aminoacids as one single chain.
Sorry for not having explained clearly in previous emails. Any suggestions?


Many thanks,
Qing


At 2017-06-23 16:24:13, "Qing Lv"  wrote:
>Dear Mark,
>
>
>Actually I had tried the method you suggested, but got such errors (pdb2gmx):
>Fatal error:
>Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
>sorting atoms.
>ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there 
>are no atom "O1" or "O2" in ILE entry; however, I never got such errors when 
>using pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal 
>residues for PDB files?
>
>
>Also, I have tried to process protein and ATP separately with pdb2gmx and then 
>combined them together, but met problems. That's why I sent another 2 emails...
>
>
>Qing
>
>
>At 2017-06-23 15:33:17, "Mark Abraham"  wrote:
>>Hi,
>>
>>I suggest you produce your initial conformation in .gro format, which
>>permits five-character atom names. That might mean using editconf on your
>>.pdb file, and then manually renaming atoms.
>>
>>Mark
>>
>>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:
>>
>>> Hi,
>>>
>>>
>>> Gromos 54a7 force field has built-in topologies for some small molecules,
>>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>>> recognized then.
>>> Anyone know how to solvate this problem? Many thanks ^_^
>>>
>>>
>>> Qing
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

Dear Mark,


Actually I had tried the method you suggested, but got such errors (pdb2gmx):
Fatal error:
Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
sorting atoms.
ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are 
no atom "O1" or "O2" in ILE entry; however, I never got such errors when using 
pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal residues 
for PDB files?


Also, I have tried to process protein and ATP separately with pdb2gmx and then 
combined them together, but met problems. That's why I sent another 2 emails...


Qing


At 2017-06-23 15:33:17, "Mark Abraham"  wrote:
>Hi,
>
>I suggest you produce your initial conformation in .gro format, which
>permits five-character atom names. That might mean using editconf on your
>.pdb file, and then manually renaming atoms.
>
>Mark
>
>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:
>
>> Hi,
>>
>>
>> Gromos 54a7 force field has built-in topologies for some small molecules,
>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>> recognized then.
>> Anyone know how to solvate this problem? Many thanks ^_^
>>
>>
>> Qing
>> --
>> 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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>> 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] Pulling inside a channel to calculate the PMF

[François-Régis Chalaoux]

Thanks Alex, finding the positions as you propose seems a legitimate way
for this problem. One will have to wait enough with a classical MD but Bias
MD should help. In my case the channel is not a large ion channel.

FR.

2017-06-22 18:26 GMT+02:00 Alex :

> I've never used PLUMED, to be honest, so I don't know.
>
> If ligands are salt ions or any other overall charged entities, I would
> solvate the channel (with restraint, maybe) for essentially a production
> run and apply an electric field "parallel" to the channel lumen, then just
> visualize the trajectory and pick the configurations by hand. gmx trjconv
> can -dump any particular frame of your liking. Maybe not as automated as
> one could hope, but then you will know in-depth what configs you have.
>
> Alex
>
>
> On 6/22/2017 3:03 AM, François-Régis Chalaoux wrote:
>
>> Hi Alex,
>>
>> There is no confusion about the pulling that is only a preparation for
>> WHAM, but as you tell it you need to choose positions. These positions
>> could be choosen manually: if one choose to explore the static channel
>> from
>> apo, then I'm agree, select the positions in the channel "in a bunch of
>> reasonably spaced spots along the curved "axis" of your channel, each
>> followed by equilibration and the production run, yielding the data useful
>> for WHAM". As you say, you need time and patience. Could PLUMED (or
>> somethoing else) /Gromacs be used to automate this ?
>>
>> On the other side, this channel come from a static APO structure and the
>> reality of this channel is tiedous, so why not discover dynamically the
>> channel and run the next equilibration and the production run on the fly,
>> could
>> PLUMED (or somethoing else)/Gromacs  be used to automate this ? How to
>> discover the channel on the fly ? May be it is feasible to use simply the
>> coordinates of the channel discovered by MDPocket with a long classical MD
>> realized  previously on the apo/holo structure ?
>>
>> FR.
>>
>> 2017-06-22 10:19 GMT+02:00 Alex :
>>
>> I think your problem is solvable with enough perseverance, but there may
>>> also be some confusion... The PMF calculation isn't based on the data
>>> obtained from an actual pull: the pulling rate in those simulations is
>>> set
>>> to zero. The reason for using pull code there is to pull (pun intended)
>>> the
>>> positions and/or forces. The initial structures, of course, is where e.g.
>>> Justin's tutorial uses pull along a straight line.
>>>
>>> However, if you have the time and patience, you could of course
>>> (manually?) put your ligand in a bunch of reasonably spaced spots along
>>> the
>>> curved "axis" of your channel, each followed by equilibration and the
>>> production run, yielding the data useful for WHAM.
>>>
>>> Hope this helps.
>>>
>>> Alex
>>>
>>>
>>> On 6/22/2017 2:05 AM, François-Régis Chalaoux wrote:
>>>
>>> Hi everybody,

 I would like to pull a ligand in a channel from my protein and calculate
 the PMF with Umbrella sampling. This channel is probably not linear and
 thus have to be defined. Too much colisions appears along a simple one
 axis
 pulling and causing a catastrophic PMF calculation.

 Currently I'm working with Gromacs and I wondered if it is possible to
 define statically or dynamically the coordinates for the center of the
 channel and use it during the simulation (Pulling).

 One solution could be to define in the md_pull.mdp configuration file
 all
 the transition points of my pathway through which my ligand must pass
 from
 my APO structure determined with CAVER.
 Instantiation of Gromacs parameters of md_pull.mdp is not enough clear
 for
 me and PLUMED is may be a more direct solution. Currently I have no
 experience with PLUMED but It seems on paper to be able.

 An other choice would be to define dynamically the channel center,
 on-the-fly. PLUMED seems also capable to manage this sort of challenge
 but
 once again I have no idea of the feasibility of a such work.


 What do you think about this problem and of the tracks evoked above ?


 Cheers, FR.

 *Pulling inside a channel to calculate the PMF*. Available from:
 https://www.researchgate.net/post/Pulling_inside_a_channel_t
 o_calculate_the_PMF#594b792648954cf7f2759a48
 [accessed Jun 22, 2017].

 --
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Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Mark Abraham]

Hi,

You can't just paste together two topology files intended to stand alone
e.g. because they have [defaults] sections. You can #include files, but
they have to follow the structure of the example in chapter 5 of the manual
(and every tutorial). Defaults, then atomtypes and parameters, then
moleculetypes, then system.

Mark

On Fri, Jun 23, 2017 at 5:47 AM Qing Lv  wrote:

> I changed the order of .itp file and put the "topol_ATP.itp" ahead of
> protein.itp . However, I got the following errors this time:
> Fatal error:
> Syntax error - File forcefield.itp, line 6
> Last line read:
> '  11   no  1.0 1.0'
> Found a second defaults directive.
>
>
> P.S.
> My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+
> (probably inappropriate) but still got the same errors.
>
>
> Thanks,
> Qing
>
>
>
> At 2017-06-23 09:46:49, "Qing Lv"  wrote:
> >Dear All,
> >
> >
> >I am setting up a simulation of protein-ATP complex. I manually combined
> the coordinates and topologies of the protein and ATP together, and ran
> editconf and solvate successfully. However, when I ran grompp, errors
> occurred:
> >Syntax error - File forcefield.itp, line 4
> >Last line read:
> >'[ defaults ]'
> >Invalid order for directive defaults
> >
> >
> >I checked the .itp files I used and did not find "[ defaults ]" pattern.
> How to fix it?
> >Thanks,
> >Qing
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Re: [gmx-users] 5-letter atom names in topology files

[Mark Abraham]

Hi,

I suggest you produce your initial conformation in .gro format, which
permits five-character atom names. That might mean using editconf on your
.pdb file, and then manually renaming atoms.

Mark

On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:

> Hi,
>
>
> Gromos 54a7 force field has built-in topologies for some small molecules,
> like ATP. In these topologies, many atoms have names of up to 5 letters,
> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
> recognized then.
> Anyone know how to solvate this problem? Many thanks ^_^
>
>
> Qing
> --
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