Re: [gmx-users] Implicit solvent improvement in Gromacs 5.1.2

[Mark Abraham]

Hi,

There's been no active work since 4.5 and no plans I've heard of. I hear
AMBER is pretty good at it on GPUs :-)

Mark

On Wed, Nov 9, 2016 at 12:04 AM Christian Bope Domilongo <
christianb...@aims.ac.za> wrote:

> Dear all,
>
> There is any improvement of GB implicit solvent in Gromacs package 5.1.2?
>
> Regards,
> --
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[gmx-users] Implicit solvent improvement in Gromacs 5.1.2

[Christian Bope Domilongo]

Dear all,

There is any improvement of GB implicit solvent in Gromacs package 5.1.2?

Regards,
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[gmx-users] sn-2 splitting

[m g]

Dear Justin Lemkul,In "kalp in dppc tutorial", why can not seen the splitting 
of the order parameter at the second carbon of sn-2 chain?
Many thanks
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[gmx-users] sn-2 splitting

[m g]

Dear Justin Lemkul,In "kalp in dppc" tutorial, why can not see the splitting of 
the order parameter at the secondcarbon of sn-2 chain?Many thanks
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[gmx-users] Md simulation error

[maria khan]

Dear justin lemkul,,
Thanks alot..i like the way u answer my stupid questions..actually i dont
have anyone to guide me except u.thats why i ask even stupid questions.dont
mind please.i want to work under your supervision because i have passion
for simulation on gromacs.
Now coming to the point,,my problem was concerned with his residue of atom
HD1.I just went to pdb file and rename that HD1 to H3.then two files formed
that are  " "posre _protein chain_A.itp  and  topol_protein_chain _A.itp""
.while  topol.top   remained empty.now it gives me another error that is
" " Residue 'IS A' not found in residue topology database"".
im using version 5.1.2 actually.
i 'll encourage and wellcome even live discussion with you.I studied your
papers on simulation.
Regards.
GOD bless you.
Maria khan
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Re: [gmx-users] REMD ensemble of states

[Mark Abraham]

Yes

On Tue, 8 Nov 2016 18:43 Abramyan, Tigran  wrote:

> Hi Mark,
>
> Thanks a lot for your prompt response. So  demux.pl creates continuous
> trajectories, *_trajout.xtc, but the ensemble of states (lowest energy
> ensemble, typically of interest in the analysis of REMD results) is saved
> in the original  0.xtc file produced during REMD before using demux.pl?
>
> Thank you,
> Tigran
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Tuesday, November 8, 2016 5:53 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REMD ensemble of states
>
> Hi,
>
> Mdrun wrote that. You made the trajectories contiguous with the demux.
>
> Mark
>
> On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  wrote:
>
> > Hi,
> >
> >
> > I conducted REMD, and extracted the trajectories via
> > trjcat -f *.trr -demux replica_index.xvg
> > And now I was wondering which *.xtc file is the ensemble of states at the
> > baseline replica (lowest temperature replica). Intuitively my guess is
> that
> > the numbers in the names of *_trajout.xtc files correspond to the replica
> > numbers starting from the baseline, and hence 0_trajout.xtc is the
> ensemble
> > of states at the baseline replica, but I may be wrong.
> >
> >
> > Please suggest.
> >
> >
> > Thank you,
> >
> > Tigran
> >
> >
> > --
> > Tigran M. Abramyan, Ph.D.
> > Postdoctoral Fellow, Computational Biophysics & Molecular Design
> > Center for Integrative Chemical Biology and Drug Discovery
> > Eshelman School of Pharmacy
> > University of North Carolina at Chapel Hill
> > Chapel Hill, NC 27599-7363
> >
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] qm/mm LA not found

[Groenhof, Gerrit]

Hi,

I could reproduce your problem and may know the reason.

I had not realised you were using Gromos force field. Normally one uses the 
gb_XX defines after each pair of bonded atoms to inform grompp of the values 
the bond parameters. See for example how it is done in your topol.top. 

Without information (i.e. bond distance and force constant) in the topology 
file, grompp cannot proceed.

You wrote it worked for 'pure' MM. I suppose that in that .itp file there are 
defines (gb_XX) or explicitly included values for bond length and force 
constant?

Best,

Gerrit




That's strange indeed. You showed a copy from the bonded section.

Which was line 133? bond 24-23?

The linkatom is defined as a virtual site and has no mass?

I can only guess, but perhaps if I can see the input files, I may understand 
quicker what goes wrong here.

Best,

gerrit





Hi Gerrit,

yes, grompp complains only about bond type 1. It gives only error for
lines where the bond types are described, nothing about angle or torsion
types.
I was able to run normal MM, as well as QM/MM if I get the whole
cofactor in QM
region, meaning if all bond types in cofactor are type 5 it runs without
problems.

Greetings
Sylwia


On 07.11.2016 14:50, Groenhof, Gerrit wrote:
> Hi,
>
> Do I understand correctly that the grompp complains about a bond that is 
> still bond type 1?
>
> If so, then the error message suggests that grompp cannot access a ff*bin.itp 
> with the parameters for the atom pair.
>
> Usually you'd also get additional errors for missing angle and torsion types. 
> Do you get those?
>
> Can you run without QM/MM, i.e. a 'normal' MM simulations with this topology?
>
> Gerrit
>
>
> Hi Gerrit,
>
> thank you for your hint. There was no LA entry in the ff*nb.it file. I
> have added it there.
> But now I get a new error. I have a protein with cofactor. Part of the
> cofactor is in QM part
> and the rest in MM. For the cofactor I have a separate *itp file as for
> the rest of protein.
> By preparing the calculation I get and error for all MM atoms:
>
> ERROR 1 [file DRGGMX_groups_v3_QMMM.itp, line 133]:
> No default Bond types
>
> example from *itp file
>
> [ bonds ]
> ; ai  aj  fuc0, c1, ...
> ...
> 21  22   5 ;   C9A  N10
> 22  23   5 ;   N10  C1' ;'
> 24  23   1 ;   C2'  C1'
> 24  25   1 ;   C2'  O2'
>
> There is no error for atoms with bond type 5, but for all with bond type 1.
>
> Greetings
> Sylwia
>
>
> On 11/05/2016 03:40 PM, Groenhof, Gerrit wrote:
>> Is the LA also defined for the force field you're using? Can you check 
>> whether there is a LA entry in the ff*nb.it of the force field? If not, add 
>> it there manually.
>>
>> Best,
>> gerrit
>>
>> Message: 2
>> Date: Fri, 4 Nov 2016 16:10:03 +0100
>> From: Sylwia Kacprzak 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] qm/mm LA not found
>> Message-ID: <581ca4cb.2050...@physchem.uni-freiburg.de>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Dear all,
>>
>> I have set qm/mm calculations with Gromacs 5.1.4 and Orca.
>> I treat first the full cofactor on a QM level. However when I cut the
>> bond to take only part of it for QM and
>> introduce link atom according to the manual with link atom (LA) I get
>> following error.
>>
>> ---
>> Program gmx grompp, VERSION 5.1.4
>> Source code file:
>> /home/widu/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line: 1345
>>
>> Fatal error:
>> Atomtype LA not found
>>
>> Any ideas?
>>
>> Greetings
>> Sylwia
>>
>>
>>
>
>
> --
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 151, Issue 22
> **




--

Message: 5
Date: Mon, 7 Nov 2016 18:06:34 + (UTC)
From: m g 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: [gmx-users] convergence
Message-ID: <951804911.2088266.1478541994...@mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Dear Justin Lemkul,what must be done for checking of convergence of the 
umbrella sampling simulations? which kind of parameter must be calculated?
Many thanks

--

Message: 6
Date: Mon, 7 Nov 2016 23:03:06 +0100
From: Szil?rd P?ll 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Can't locate AMD SDK opencl, among else,
during compile
Message-ID:

Re: [gmx-users] REMD ensemble of states

[Abramyan, Tigran]

Hi Mark,

Thanks a lot for your prompt response. So  demux.pl creates continuous 
trajectories, *_trajout.xtc, but the ensemble of states (lowest energy 
ensemble, typically of interest in the analysis of REMD results) is saved in 
the original  0.xtc file produced during REMD before using demux.pl?

Thank you,
Tigran


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

Sent: Tuesday, November 8, 2016 5:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states

Hi,

Mdrun wrote that. You made the trajectories contiguous with the demux.

Mark

On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  wrote:

> Hi,
>
>
> I conducted REMD, and extracted the trajectories via
> trjcat -f *.trr -demux replica_index.xvg
> And now I was wondering which *.xtc file is the ensemble of states at the
> baseline replica (lowest temperature replica). Intuitively my guess is that
> the numbers in the names of *_trajout.xtc files correspond to the replica
> numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble
> of states at the baseline replica, but I may be wrong.
>
>
> Please suggest.
>
>
> Thank you,
>
> Tigran
>
>
> --
> Tigran M. Abramyan, Ph.D.
> Postdoctoral Fellow, Computational Biophysics & Molecular Design
> Center for Integrative Chemical Biology and Drug Discovery
> Eshelman School of Pharmacy
> University of North Carolina at Chapel Hill
> Chapel Hill, NC 27599-7363
>
> --
> 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] oplsaa HISE is charged in gmx 5.1.4 and 2016

[Jon Kapla]

Thanks Mark and Justin,

I'll have a go at 2016.1 then.

Cheers,
Jon

 Mark Abraham skrev 

Hi,

Actually
http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/release-notes.html#fixed-opls-aa-l-charges-for-hisd-and-hise
refers
to David's first fix of https://redmine.gromacs.org/issues/2013, which was
indeed incorrect in this aspect. Justin has since fixed that, but after
5.1.4 was released. That fix will be in 5.1.5 if/when we make one. However,
you can feel quite comfortable about taking the 2016.1 share/top/oplsaa.ff
directory and using it with 5.1.x.

Mark

On Tue, Nov 8, 2016 at 4:03 PM Justin Lemkul  wrote:

>
>
> On 11/8/16 9:54 AM, Jon Kapla wrote:
> > Hi everyone,
> >
> > I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When
> running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a
> specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same
> protonation, but a more reasonable integer charge of 3e.
> >
> > I have investigated the issue, and it seems that the difference is
> stemming from differing atom charges in the HISE residue in aminoacids.rtp.
> If I sum up the atom charges in HISE (5.1.4) I find that it actually is
> charged by -0.113e, which exatly corresponds to the difference in the
> reported charge from pdb2gmx (5 HISE * -0.113).
> >
> > Is this a known problem?
> >
>
> This should have been fixed for 5.1.4 (and the release notes say it was),
> but
> clearly the files are incorrect.  The charges are correct in 2016.1 so
> please
> use that version.
>
> -Justin
>
> > Cheers,
> > Jon
> > --
> > Postdoc, Carlsson lab
> > Dept. of Cell and Molecular Biology, Computational Biology and
> Bioinformatics
> >
> > Uppsala Biomedicinska Centrum BMC, Husarg. 3
> > Box 596
> > S-751 24, Uppsala
> >
> > E-mail: jon.ka...@icm.uu.se
> > Phone: +46 70 3041989 <070-304%2019%2089>
> >
>
> --
> ==
>
> 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] binding free energy with gromacs2016

[Justin Lemkul]

On 11/8/16 11:00 AM, Qasim Pars wrote:

Dear users,

Hope someone will answer the questions in my previous mail.

Thanks in advance,


On 6 Nov 2016, at 23:48, Qasim Pars  wrote:

Dear users,

I will try to do binding free energy calculation using GROMACS2016 but I am 
confused a little bit about the preparation of  the input files. I have a few 
questions:

1) There are below lines to apply a harmonic distance restraint in the mdp 
files of the binding free energy tutorial 
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

pull   = umbrella
pull_geometry  = distance
pull_dim   = Y Y Y
pull_start = no
pull_init1 = 0.654
pull_ngroups   = 1
pull_group0= a_1391
pull_group1= a_2615
pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)

Question 1: Instead of those lines I would like to use the [ 
intermolecular_interactions ] section in the topology file with GROMACS2016. 
Could you please tell me what to write the [ intermolecular_interactions ] 
section?



Why?  The pull code is modulated in a lambda-dependent fashion, which is 
probably part of the tutorial and computed free energy.



2) complex.top file of the tutorial is as follows:
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

[ atomtypes ]
;name  bond_type  masscharge  ptype   sigma  epsilon
c3c3  0.  0.  A   3.39967e-01  4.57730e-01
dc3   c3  0.  0.  A   0.0e+00  0.0e+00


Question 2: Why all values (sigma and epsilon) of dc3 are zero?



This is effectively a dummy atom, used in transforming the ligand.


[ nonbond_params ]
; i  jfunc  sigma   epsilon
c3   c31 3.3996700e-01   4.5773000e-01
dc3  dc3   1 3.3996700e-01   4.5773000e-01

Question 3: Why all values of dc3 aren't zero?



These are pair-specific interactions.


[ angle_restraints ]
; ai ajakaltype thA  kA multA  thB  kB  
   multB
 1393   1391   2615  1391  188.8 0.00   1  88.8 
41.84   1
 1391   2615   2614  2615  132.9 0.00   1  32.9 
41.84   1

[ dihedral_restraints ]
; aiajakal   type   phiA dphiA   kA  phiB dphiB 
  kB
  1410  1393  1391  2615 1  -159.7  0.0  0.00-159.7   0.0   
  41.84
  1393  1391  2615  2614 1  122.6   0.0  0.00 122.6   0.0   
  41.84
  1391  2615  2614  2610 1  12.80.0  0.00  12.8   0.0   
  41.84
.
Question 4: Do I still need to put those ligand parameters (dc3, [ 
angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to use 
with GROMACS2016?



There is no version-dependent difference here with respect to the topology.

-Justin


I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't 
understand how to prepare the input files.
--
Qasim Pars


--
==

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] oplsaa HISE is charged in gmx 5.1.4 and 2016

[Mark Abraham]

Hi,

Actually
http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/release-notes.html#fixed-opls-aa-l-charges-for-hisd-and-hise
refers
to David's first fix of https://redmine.gromacs.org/issues/2013, which was
indeed incorrect in this aspect. Justin has since fixed that, but after
5.1.4 was released. That fix will be in 5.1.5 if/when we make one. However,
you can feel quite comfortable about taking the 2016.1 share/top/oplsaa.ff
directory and using it with 5.1.x.

Mark

On Tue, Nov 8, 2016 at 4:03 PM Justin Lemkul  wrote:

>
>
> On 11/8/16 9:54 AM, Jon Kapla wrote:
> > Hi everyone,
> >
> > I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When
> running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a
> specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same
> protonation, but a more reasonable integer charge of 3e.
> >
> > I have investigated the issue, and it seems that the difference is
> stemming from differing atom charges in the HISE residue in aminoacids.rtp.
> If I sum up the atom charges in HISE (5.1.4) I find that it actually is
> charged by -0.113e, which exatly corresponds to the difference in the
> reported charge from pdb2gmx (5 HISE * -0.113).
> >
> > Is this a known problem?
> >
>
> This should have been fixed for 5.1.4 (and the release notes say it was),
> but
> clearly the files are incorrect.  The charges are correct in 2016.1 so
> please
> use that version.
>
> -Justin
>
> > Cheers,
> > Jon
> > --
> > Postdoc, Carlsson lab
> > Dept. of Cell and Molecular Biology, Computational Biology and
> Bioinformatics
> >
> > Uppsala Biomedicinska Centrum BMC, Husarg. 3
> > Box 596
> > S-751 24, Uppsala
> >
> > E-mail: jon.ka...@icm.uu.se
> > Phone: +46 70 3041989 <070-304%2019%2089>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] Md simulation of protein ligand error.

[Justin Lemkul]

On 11/8/16 10:15 AM, maria khan wrote:

Dear justin..
  My problem of protein ligand simulation , regarding protonation states
for His residue has solved..now that error exists no more.There are two
things that i want to share,,one is that i didnot get how that problem
solved,i just followed that manuals while i have no idea how it just
solved..secondly it gives furthur another error that says that is
"software inconsistancy error"can u kindly guide me please,


There is nothing anyone can do to help you without an exact description of what 
you're doing - what version you're using, exact commands, exact screen output 
(everything copied and pasted from the terminal).


-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] Md simulation of protein ligand error.

[maria khan]

Dear justin..
  My problem of protein ligand simulation , regarding protonation states
for His residue has solved..now that error exists no more.There are two
things that i want to share,,one is that i didnot get how that problem
solved,i just followed that manuals while i have no idea how it just
solved..secondly it gives furthur another error that says that is
"software inconsistancy error"can u kindly guide me please,
 regards and thanks alot for your coperation.
  Maria khan.
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Re: [gmx-users] binding free energy with gromacs2016

[Qasim Pars]

Dear users,

Hope someone will answer the questions in my previous mail.

Thanks in advance,

> On 6 Nov 2016, at 23:48, Qasim Pars  wrote:
> 
> Dear users,
> 
> I will try to do binding free energy calculation using GROMACS2016 but I am 
> confused a little bit about the preparation of  the input files. I have a few 
> questions:
> 
> 1) There are below lines to apply a harmonic distance restraint in the mdp 
> files of the binding free energy tutorial 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> pull   = umbrella 
> pull_geometry  = distance
> pull_dim   = Y Y Y
> pull_start = no
> pull_init1 = 0.654
> pull_ngroups   = 1
> pull_group0= a_1391
> pull_group1= a_2615
> pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
> pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)
> 
> Question 1: Instead of those lines I would like to use the [ 
> intermolecular_interactions ] section in the topology file with GROMACS2016. 
> Could you please tell me what to write the [ intermolecular_interactions ] 
> section? 
> 
> 2) complex.top file of the tutorial is as follows:
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> 
> [ atomtypes ]
> ;name  bond_type  masscharge  ptype   sigma  epsilon
> c3c3  0.  0.  A   3.39967e-01  4.57730e-01
> dc3   c3  0.  0.  A   0.0e+00  0.0e+00
> 
> 
> Question 2: Why all values (sigma and epsilon) of dc3 are zero? 
> 
> [ nonbond_params ]
> ; i  jfunc  sigma   epsilon
> c3   c31 3.3996700e-01   4.5773000e-01
> dc3  dc3   1 3.3996700e-01   4.5773000e-01
> 
> Question 3: Why all values of dc3 aren't zero? 
> 
> [ angle_restraints ]
> ; ai ajakaltype thA  kA multA  thB  
> kB multB
>  1393   1391   2615  1391  188.8 0.00   1  88.8 
> 41.84   1  
>  1391   2615   2614  2615  132.9 0.00   1  32.9 
> 41.84   1 
> 
> [ dihedral_restraints ]
> ; aiajakal   type   phiA dphiA   kA  phiB 
> dphiB   kB
>   1410  1393  1391  2615 1  -159.7  0.0  0.00-159.7   0.0 
> 41.84
>   1393  1391  2615  2614 1  122.6   0.0  0.00 122.6   0.0 
> 41.84
>   1391  2615  2614  2610 1  12.80.0  0.00  12.8   0.0 
> 41.84
> .
> Question 4: Do I still need to put those ligand parameters (dc3, [ 
> angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to 
> use with GROMACS2016?
> 
> I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't 
> understand how to prepare the input files.
> -- 
> Qasim Pars
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[gmx-users] g_wham error in umbrella simulation

[diana p]

Dear all
I am doing an umbrella simulation by using the pull code in Gromacs
4.6.5 to calculate the PMF. The pull parameters are the following:

;Pull code
pull= constant_force
pull_geometry  = position
pull_dim= N N Ypull_start   = no
pull_ngroups = 1pull_group0   = GRApull_group1   =
UNKpull_rate1  = 0.01 pull_k1  = 1000
pull_vec1  = 0.0 0.0 1.0

When i run the WHAM with the Command line:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
it gave me the following error:

Fatal error: This is not a tpr of an umbrella simulation. Found pull type
"constant-force" (ir.ePull= 3)

I would be more than pleased if someone could guid me.
Thank You in advance
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Re: [gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016

[Justin Lemkul]

On 11/8/16 9:54 AM, Jon Kapla wrote:

Hi everyone,

I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When running 
pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a specific GPCR 
ends up at 2.435e. Running gromacs 4.6.7 results in the same protonation, but a 
more reasonable integer charge of 3e.

I have investigated the issue, and it seems that the difference is stemming 
from differing atom charges in the HISE residue in aminoacids.rtp. If I sum up 
the atom charges in HISE (5.1.4) I find that it actually is charged by -0.113e, 
which exatly corresponds to the difference in the reported charge from pdb2gmx 
(5 HISE * -0.113).

Is this a known problem?



This should have been fixed for 5.1.4 (and the release notes say it was), but 
clearly the files are incorrect.  The charges are correct in 2016.1 so please 
use that version.


-Justin


Cheers,
Jon
--
Postdoc, Carlsson lab
Dept. of Cell and Molecular Biology, Computational Biology and Bioinformatics

Uppsala Biomedicinska Centrum BMC, Husarg. 3
Box 596
S-751 24, Uppsala

E-mail: jon.ka...@icm.uu.se
Phone: +46 70 3041989



--
==

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] oplsaa HISE is charged in gmx 5.1.4 and 2016

[Jon Kapla]

Hi everyone,

I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When running 
pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a specific GPCR 
ends up at 2.435e. Running gromacs 4.6.7 results in the same protonation, but a 
more reasonable integer charge of 3e.

I have investigated the issue, and it seems that the difference is stemming 
from differing atom charges in the HISE residue in aminoacids.rtp. If I sum up 
the atom charges in HISE (5.1.4) I find that it actually is charged by -0.113e, 
which exatly corresponds to the difference in the reported charge from pdb2gmx 
(5 HISE * -0.113).

Is this a known problem?

Cheers,
Jon
--
Postdoc, Carlsson lab
Dept. of Cell and Molecular Biology, Computational Biology and Bioinformatics

Uppsala Biomedicinska Centrum BMC, Husarg. 3
Box 596
S-751 24, Uppsala

E-mail: jon.ka...@icm.uu.se
Phone: +46 70 3041989

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Re: [gmx-users] g_wham error in umbrella simulation

[Justin Lemkul]

On 11/8/16 9:50 AM, diana p wrote:

Dear all
I am doing an umbrella simulation by using the pull code in Gromacs
4.6.5 to calculate the PMF. The pull parameters are the following:

;Pull code
pull= constant_force
pull_geometry  = position
pull_dim= N N Ypull_start   = no
pull_ngroups = 1pull_group0   = GRApull_group1   =
UNKpull_rate1  = 0.01 pull_k1  = 1000
pull_vec1  = 0.0 0.0 1.0

When i run the WHAM with the Command line:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
it gave me the following error:

Fatal error: This is not a tpr of an umbrella simulation. Found pull type
"constant-force" (ir.ePull= 3)

I would be more than pleased if someone could guid me.


The error is pretty explicit - you didn't do umbrella sampling.  You applied a 
constant biasing force.  To do umbrella sampling, you need "pull = umbrella" 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] (no subject)

[Justin Lemkul]

On 11/8/16 6:13 AM, Kingsley Theras Primus Dass . wrote:

Even when I add the new atom types to aminoacid.rtp, .hdb ,   .atp ,
Still it shows the same error 



The error has nothing to do with atom types, and without seeing what you did, 
there's no possible way to solve it.  An anionic sulfotyrosine residue should 
have the same .hdb entry as normal tyrosine.  Copy it and rename the residue to 
whatever your .rtp specifies.


-Justin


Could you please suggest some solutions.

Thank you in advance

On 8 Nov 2016 6:59 p.m., "Justin Lemkul"  wrote:




On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:


Hello users!!

I generated a Topology file for SO3- using ATB topology generator , which
is compatible with GROMACS. Then I copied the .rtp file from ATB and
pasted
it into  GROMACS aminoacid.rtp.

 The  partial charge of aminoacid sulfated-tyrosine was -1.
When I run -pdb2gmx there was error saying the atoms were missing ,
---
Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce
ss/pdb2top.cpp,
line: 1584

Fatal error:
There were 6 missing atoms in molecule Protein_chain_D, if you want to use
this incomplete topology anyhow, use the option -missing


then I ran pdb2gmx -ignh -p topol.top -missing

It generated the topology file. But the parital charge of sulfated
tyrosine
was changed to -2, coz of missing hydrogen atoms.

can you please suggest some solutions , to overcome this problem.



Add an .hdb entry for your residue so that pdb2gmx will build the missing
atoms.  In general, never use the -missing option.

-Justin

--
==

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

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

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

==
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--
==

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

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

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

==
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Re: [gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Even when I add the new atom types to aminoacid.rtp, .hdb ,   .atp ,
Still it shows the same error 

Could you please suggest some solutions.

Thank you in advance

On 8 Nov 2016 6:59 p.m., "Justin Lemkul"  wrote:

>
>
> On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
>
>> Hello users!!
>>
>> I generated a Topology file for SO3- using ATB topology generator , which
>> is compatible with GROMACS. Then I copied the .rtp file from ATB and
>> pasted
>> it into  GROMACS aminoacid.rtp.
>>
>>  The  partial charge of aminoacid sulfated-tyrosine was -1.
>> When I run -pdb2gmx there was error saying the atoms were missing ,
>> ---
>> Program gmx pdb2gmx, VERSION 5.1
>> Source code file:
>> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce
>> ss/pdb2top.cpp,
>> line: 1584
>>
>> Fatal error:
>> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
>> this incomplete topology anyhow, use the option -missing
>>
>>
>> then I ran pdb2gmx -ignh -p topol.top -missing
>>
>> It generated the topology file. But the parital charge of sulfated
>> tyrosine
>> was changed to -2, coz of missing hydrogen atoms.
>>
>> can you please suggest some solutions , to overcome this problem.
>>
>>
> Add an .hdb entry for your residue so that pdb2gmx will build the missing
> atoms.  In general, never use the -missing option.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:

Hello users!!

I generated a Topology file for SO3- using ATB topology generator , which
is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted
it into  GROMACS aminoacid.rtp.

 The  partial charge of aminoacid sulfated-tyrosine was -1.
When I run -pdb2gmx there was error saying the atoms were missing ,
---
Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2top.cpp,
line: 1584

Fatal error:
There were 6 missing atoms in molecule Protein_chain_D, if you want to use
this incomplete topology anyhow, use the option -missing


then I ran pdb2gmx -ignh -p topol.top -missing

It generated the topology file. But the parital charge of sulfated tyrosine
was changed to -2, coz of missing hydrogen atoms.

can you please suggest some solutions , to overcome this problem.



Add an .hdb entry for your residue so that pdb2gmx will build the missing atoms. 
 In general, never use the -missing option.


-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] How to restart mdrun at a specific time from checkpoint

[Justin Lemkul]

On 11/7/16 11:37 PM, 张慧玲 wrote:

But the -cpi option will restart mdrun from checkpoint  at time 46840ps, I want 
to start from a previous time, for example 45000ps.



Then you need to use the -cpi option to specify the name of the checkpoint file 
that contains the state at 45000 ps.


-Justin



Hui


Message: 4
Date: Mon, 7 Nov 2016 22:14:47 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to restart mdrun at a specific time from
 checkpoint
Message-ID: 
Content-Type: text/plain; charset=UTF-8; format=flowed



On 11/7/16 10:01 PM, ??? wrote:

Hi,
my mdrun stopped at 46840ps, I want to restart the mdrun at 45000ps from 
checkpoint. How could I told the mdrun to do this???


Supply that checkpoint file to mdrun -cpi.

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

-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] REMD ensemble of states

[Mark Abraham]

Hi,

Mdrun wrote that. You made the trajectories contiguous with the demux.

Mark

On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  wrote:

> Hi,
>
>
> I conducted REMD, and extracted the trajectories via
> trjcat -f *.trr -demux replica_index.xvg
> And now I was wondering which *.xtc file is the ensemble of states at the
> baseline replica (lowest temperature replica). Intuitively my guess is that
> the numbers in the names of *_trajout.xtc files correspond to the replica
> numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble
> of states at the baseline replica, but I may be wrong.
>
>
> Please suggest.
>
>
> Thank you,
>
> Tigran
>
>
> --
> Tigran M. Abramyan, Ph.D.
> Postdoctoral Fellow, Computational Biophysics & Molecular Design
> Center for Integrative Chemical Biology and Drug Discovery
> Eshelman School of Pharmacy
> University of North Carolina at Chapel Hill
> Chapel Hill, NC 27599-7363
>
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Re: [gmx-users] How to restart mdrun at a specific time from checkpoint

[Mark Abraham]

Hi,

You can start from any cpt you have, but each file contains only one
snapshot. So you can't arbitrarily restart unless you saved cpt files
manually. Using mdrun -noappend is a good way to do this, but leaves you
with manual work to do concatenating files for your analysis. Or archive
your cpt files between runs. But be aware that you will not generally be
able to repeat the same trajectory from any checkpoint, so only do this if
you have an appropriate reason.

Mark

On Tue, 8 Nov 2016 05:45 张慧玲  wrote:

>
>
> But the -cpi option will restart mdrun from checkpoint  at time 46840ps, I
> want to start from a previous time, for example 45000ps.
>
>
> Hui
> >
> > Message: 4
> > Date: Mon, 7 Nov 2016 22:14:47 -0500
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] How to restart mdrun at a specific time from
> >  checkpoint
> > Message-ID: 
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> >
> >
> > On 11/7/16 10:01 PM, ??? wrote:
> > > Hi,
> > > my mdrun stopped at 46840ps, I want to restart the mdrun at
> 45000ps from checkpoint. How could I told the mdrun to do this???
> >
> > Supply that checkpoint file to mdrun -cpi.
> >
> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
> >
> > -Justin
> >
>
>
>
>
>
>
>
>
>
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