Re: [gmx-users] DSSP

[Vytautas Rakeviius]

ftp://ftp.cmbi.ru.nl/pub/software/dssp/
There you can find windows .exe version of it.
 

On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R 
 wrote:  
 
 Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
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[gmx-users] DSSP

[Vidya R]

Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
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Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Justin Lemkul]

On 12/4/17 2:35 PM, Daniel Bauer wrote:

Unfortunatly It seems like my university has no contract to access this
paper so I cant check the SI.

The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted
to better match the free energy of solvation in NMA).


There seem to be several layers of assumption here, including targeting 
a value that is actually unknown.


If you want to compare, in the paper I linked before, we did a QM 
potential energy scan for NMA...K+ as a function of the distance between 
the carbonyl O and the ion. The standard CHARMM force field parameters 
are too weak by about 6 kcal/mol relative to an MP2/6-311++G(2df,2pd) 
energy surface. The NBFIX we applied to correct it was:


epsilon = -0.050218 kcal/mol
Rmin = 3.30375 A

-Justin



On  12/04/2017 07:53 PM, Justin Lemkul wrote:


On 12/4/17 12:21 PM, Daniel Bauer wrote:

Hello,

I finally found my error in the conversion. As always, the devil is in
the detail. I was under the assumption that parameters listed in the
original forcefield files (toppar) are also sigma and epsilon values.
However, as you know, the original files list Rmin values (and not
sigma).

With the correct conversion term:

eps = Rmin/(10*2^(1/6))

I can now reproduce the conversion of the numbers from the charmm
implementation to gromacs (and thus know how to apply my NBFIX for this
value).

I don't know what NBFIX you might have, but FYI there is a value that
will become official in the next release of the force field. We've
validated it against proteins and nucleic acids. See the SI of
http://dx.doi.org/10.1128/AAC.01572-17

-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] Problem with topology generation by Amber 12 ff

[Amir Zeb]

Thanks Dr. Justin,

The atoms of Histidine residue formed the dihedral CB, CG, ND1 and CD2.
Tracing the residues rtp file in Amber12 ff, I should assign His either HID
or HIE, But once I protonate HIS at NE2 only and assign this NE2-protonated
HIS as HIE, some of the residues other than this particular HIS also read
as HIE by the force filed itself and I should assign them as HIE, because
otherwise I will get the same error as mentioned above.

Thanks for your consideration!

On Mon, Dec 4, 2017 at 6:25 AM, Justin Lemkul  wrote:

>
>
> On 12/4/17 1:45 AM, Amir Zeb wrote:
>
>> Hello gmx users,
>>
>> I have generated topology and coordinate files of ZN metalloprotein by
>> Amber 12 ff. Now I am facing this following issue at grompp run:
>>
>> "ERROR 1 [file topol_Protein_chain_A.itp, line 49741]:
>>No default Improper Dih. types"
>>
>> If I use another ff like Amber99SB- ILDN, there is no such error. I
>> searched out the solution on google but could not find the answer.
>>
>> Please help me how to fix this issue?
>>
>
> Which atoms are in that interaction on that line, and should there be such
> an interaction 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] request

[Dallas Warren]

The error states what the problem is, there are three files that the
program expects to be in the directory, but they aren't.

Two things can do, change the command line if it is doing not what you
want it to (i.e. it is trying to add more data onto an existing
simulation, or you have used the wrong file names) or return the files
to the directory so that it can append data to them.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 5 December 2017 at 06:32, Rakesh Pant
 wrote:
> What is -s md ? in the command line.
>
> On 05-Dec-2017 12:32 AM,  wrote:
>
> hi.what causes this error?
>
> Command line:
> gmx mdrun -s md -cpi md_0_1_prev.cpt
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md_0_1_prev.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
>
> Expected output files not present or named differently:
> md_0_1.log
> md_0_1.xtc
> md_0_1.edr
>
> ---
> Program: gmx mdrun, version 2016.3
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
>
> Fatal error:
> File appending requested, but 3 of the 3 output files are not present or
> are
> named differently. For safety reasons, GROMACS-2016 and later only
> allows file
> appending to be used when all files have the same names as they had in
> the
> original run. Checkpointing is merely intended for plain continuation of
> runs.
> For safety reasons you must specify all file names (e.g. with -deffnm),
> and
> all these files must match the names used in the run prior to
> checkpointing
> since we will append to them by default. If the files are not available,
> you
> can add the -noappend flag to mdrun and write separate new parts. For
> mere
> concatenation of files, you should use the gmx trjcat tool instead.
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Daniel Bauer]

Unfortunatly It seems like my university has no contract to access this
paper so I cant check the SI.

The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted
to better match the free energy of solvation in NMA).


On  12/04/2017 07:53 PM, Justin Lemkul wrote:
>
>
> On 12/4/17 12:21 PM, Daniel Bauer wrote:
>> Hello,
>>
>> I finally found my error in the conversion. As always, the devil is in
>> the detail. I was under the assumption that parameters listed in the
>> original forcefield files (toppar) are also sigma and epsilon values.
>> However, as you know, the original files list Rmin values (and not
>> sigma).
>>
>> With the correct conversion term:
>>
>> eps = Rmin/(10*2^(1/6))
>>
>> I can now reproduce the conversion of the numbers from the charmm
>> implementation to gromacs (and thus know how to apply my NBFIX for this
>> value).
>
> I don't know what NBFIX you might have, but FYI there is a value that
> will become official in the next release of the force field. We've
> validated it against proteins and nucleic acids. See the SI of
> http://dx.doi.org/10.1128/AAC.01572-17
>
> -Justin
>

-- 

Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.

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Re: [gmx-users] request

[Rakesh Pant]

What is -s md ? in the command line.

On 05-Dec-2017 12:32 AM,  wrote:

hi.what causes this error?

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
md_0_1.log
md_0_1.xtc
md_0_1.edr

---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 3 of the 3 output files are not present or
are
named differently. For safety reasons, GROMACS-2016 and later only
allows file
appending to be used when all files have the same names as they had in
the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm),
and
all these files must match the names used in the run prior to
checkpointing
since we will append to them by default. If the files are not available,
you
can add the -noappend flag to mdrun and write separate new parts. For
mere
concatenation of files, you should use the gmx trjcat tool instead.
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] FaQ paramters for ADP topology with acpype

[Robert König]

Dear users,
I used acpype to  get a topology for ADP.While minimizing energy one hydrogen 
moves too much to an oxygen, ending with the oxygen "swallowing" the hydrogen 
totally. They got exact the same coordinates in the .gro output.
In the topology the parameters for that H (h0) are missing:
[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   
Amb... h1   h1  0.0  0.0   A 2.47135e-01   6.56888e-02 
; 1.39  0.0157
 ho   ho  0.0  0.0   A 0.0e+00   0.0e+00 ; 0.00 
 0.
 h2   h2  0.0  0.0   A 2.29317e-01   6.56888e-02 ; 1.29 
 0.0157...
I found parameters (ho   ho  0.0  0.0   A 1.06908e-01   
6.56888e-02 ; 0.00  0.) in the wiki (last 
question):https://code.google.com/archive/p/acpype/wikis/FAQ.wiki
Can someone confirm these parameters since there is no source.
Best regards,olaf

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[gmx-users] request

[mmahmoudig]

hi.what causes this error? 

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt 

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.cpt
are not present or not named as the output files by the current program:
Expect output files present: 

Expected output files not present or named differently:
md_0_1.log
md_0_1.xtc
md_0_1.edr 

---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177) 

Fatal error:
File appending requested, but 3 of the 3 output files are not present or
are
named differently. For safety reasons, GROMACS-2016 and later only
allows file
appending to be used when all files have the same names as they had in
the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm),
and
all these files must match the names used in the run prior to
checkpointing
since we will append to them by default. If the files are not available,
you
can add the -noappend flag to mdrun and write separate new parts. For
mere
concatenation of files, you should use the gmx trjcat tool instead.
-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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[gmx-users] request

[mmahmoudig]

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt 

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.cpt
are not present or not named as the output files by the current program:
Expect output files present: 

Expected output files not present or named differently:
md_0_1.log
md_0_1.xtc
md_0_1.edr 

---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177) 

Fatal error:
File appending requested, but 3 of the 3 output files are not present or
are
named differently. For safety reasons, GROMACS-2016 and later only
allows file
appending to be used when all files have the same names as they had in
the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm),
and
all these files must match the names used in the run prior to
checkpointing
since we will append to them by default. If the files are not available,
you
can add the -noappend flag to mdrun and write separate new parts. For
mere
concatenation of files, you should use the gmx trjcat tool instead.
-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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[gmx-users] Same parameters for ADP single P-O bonds and double P=O bonds in in acpype (GAFF) topology

[Robert König]

Dear users,
I try to simualte PKAC with 1 Mg and ADP (4ntt.pdb).For PKAC and Mg topology I 
use the GROMACS-2016.3 AMBER99SB-ILDN.
For ADP I try to use acpype. 
The H were assigned with pymol, only getting one at the phosphate groups what 
should be ok.Nevertheless acpype assigns the same paramters to the P-O single 
and P=O duoble bonds.
acpype topology output:
[ bonds ]
;   ai aj funct   r k
 1  4   1    1.6020e-01    2.8660e+05 ; PA - O5'   
 1 13   1    1.4810e-01    4.0811e+05 ; PA - O1A   
 1 16   1    1.4810e-01    4.0811e+05 ; PA - O2A   
 1 19   1    1.6020e-01    2.8660e+05 ; PA - O3A   
 2 14   1    1.6250e-01    2.6878e+05 ; PB - O1B   
 2 17   1    1.4810e-01    4.0811e+05 ; PB - O2B   
 2 19   1    1.6020e-01    2.8660e+05 ; PB - O3A   
 2 20   1    1.4810e-01    4.0811e+05 ; PB - O3B   
 3  4   1    1.4390e-01    2.5230e+05 ;    C5' - O5'   

This is what the structure looks like (projected to 2D):    
  
    H - O1B   O1A
    | ||
 O3B - PB - O3A - PA - O5' - C5' - ...
    ||    |
 O2B    O2A
The paramters should also depend on the bond type so I am not sure if this 
output is right. 
In the input .mol2 file the double bonds are assigned like in the structure 
above.Pymol shows only single bonds investigating the acpype output.
So what can I do to assign the double bonds correctly. Is it possible with 
acpype? Or doens't it matter?
Thanks for your help!
Best regards,olaf
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[gmx-users] request

[mmahmoudig]

hi.what causes this error? 

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt 

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.cpt
are not present or not named as the output files by the current program:
Expect output files present: 

Expected output files not present or named differently:
md_0_1.log
md_0_1.xtc
md_0_1.edr 

---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177) 

Fatal error:
File appending requested, but 3 of the 3 output files are not present or
are
named differently. For safety reasons, GROMACS-2016 and later only
allows file
appending to be used when all files have the same names as they had in
the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm),
and
all these files must match the names used in the run prior to
checkpointing
since we will append to them by default. If the files are not available,
you
can add the -noappend flag to mdrun and write separate new parts. For
mere
concatenation of files, you should use the gmx trjcat tool instead.
-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Justin Lemkul]

On 12/4/17 12:21 PM, Daniel Bauer wrote:

Hello,

I finally found my error in the conversion. As always, the devil is in
the detail. I was under the assumption that parameters listed in the
original forcefield files (toppar) are also sigma and epsilon values.
However, as you know, the original files list Rmin values (and not sigma).

With the correct conversion term:

eps = Rmin/(10*2^(1/6))

I can now reproduce the conversion of the numbers from the charmm
implementation to gromacs (and thus know how to apply my NBFIX for this
value).


I don't know what NBFIX you might have, but FYI there is a value that 
will become official in the next release of the force field. We've 
validated it against proteins and nucleic acids. See the SI of 
http://dx.doi.org/10.1128/AAC.01572-17


-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] lost particles while sorting

[soumadwip ghosh]

​​Hi,

I am running NPT equilibration on gpu. After I finished the NVT I got an
error saying

Software Inconsistency Error:

Lost particles while sorting (6 out of 8)

Now I looked into the archive and it seems like a bug which was fixed in
gromacs versions > 5.0. I am using gromacs-2016.4 and the error is
sporadic. It means for a slightly different system (a mutation of the
protein under consideration, almost identical in overall system size) the
simulation runs fine on the same gpu using gromacs-2016.4. I have tried to
run the buggy one by creating a tpr file using gromacs 5.1.0 but no luck
yet. How do I fix this?

I am uploading the .tpr (gromacs 2016.4) and .mdp file in the following
link.

I am looking forward to your help

https://drive.google.com/file/d/1wfQdbTqkIEnfUE81IDb5iATkFyedP2in/view?usp=sharing

https://drive.google.com/file/d/1iFskowIggdFkNlJwkQJ_LbeumV-QtUZ2/view?usp=sharing

Regards,
Soumadwip Ghosh
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Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Daniel Bauer]

Hello,

I finally found my error in the conversion. As always, the devil is in
the detail. I was under the assumption that parameters listed in the
original forcefield files (toppar) are also sigma and epsilon values.
However, as you know, the original files list Rmin values (and not sigma).

With the correct conversion term:

eps = Rmin/(10*2^(1/6))

I can now reproduce the conversion of the numbers from the charmm
implementation to gromacs (and thus know how to apply my NBFIX for this
value).

Thanks for your patience and best regards,

Daniel


On 12/03/2017 10:18 PM, Daniel Bauer wrote:
> Hello,
>
>
> I compared the LJ parameters for the interaction Potassium - backbone
> carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
> forcefield. I found different numbers for the sigma value i cannot
> explain to myself:
>
>
> The stock charmm36 implementation has the following LJ parameters for
> potassium and oxygen:
>
> ; atomEmin (kcal/mol)Rmin/2 (A)
>
> POT0.0871.76375
>
> O0.1201.7
>
>
> Converting the above values to units used in gromacs (kJ/mol and nm) and
> applying standard combination rules this should give the following
> nonbonded energy parameters:
>
> [ pairtypes]
>
> ; sig = (Rmin,i/2 + Rmin,j/2)/10
>
> ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ
>
> ; ijfuncsig (nm)eps (kj/mol)
>
> OPOT10.346 0.4275
>
> However, the actual entry for the interaction in GROMACS/charmm36 has
> the energy minimum at a much smaller distance (epsilon is on the point
> though!)
>
> ; ij func sig (nm)eps (kJ/mol)
>
> OPOT10.2820.4275
>
>
> Can somebody tell me the reason for this huge difference? Is there an
> error in my calculation? I am trying to convert an NBFIX applied to this
> specific interaction to gromacs. However, I am not sure how to proceed
> without doing the reparametrization in gromacs again, because the stock
> values differ that much.
>
> Best regards,
>
> Daniel
>
>

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.


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[gmx-users] g_sham experimental weighting with temperature

[Yasser Bruno Ruiz Blanco]

Hi,


I hope someone can suggest me any reference or description about the
mentioned "experimental energy and temperature weighting" of the tool
g_sham.

Can I safely use this weighting procedure to obtain reliable PMF plots from
a T-REMD simulation?

In case of using g_sham with the weighting option, would be better to apply
the weighting using the Total energy and the Temperature of structures from
different replicas, or only the Potential energy of the structures sampled
at the temperature of interest?

Thanks in advance for your suggestions!
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Re: [gmx-users] one protein and 4 ligands

[Justin Lemkul]

On 12/3/17 11:27 PM, Mahboobeh Eslami wrote:

Dear justinThank you so muchI did MD simulation on some protein-ligand 
complexes but I don't know that I must use one mol2 file for 4 ligands or  
separate mol2 files for each ligand. I want to calculate free energy value for 
this complex by GMXPBSA script. Must free energy value be calculated for 4 
lignads simultaneously? or I can calculate free energy value for each lignad 
individually.Thank you for kindness


No idea. How do people deal with such a situation in the literature?

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] request

[Justin Lemkul]

On 12/3/17 11:40 PM, mmahmou...@razi.tums.ac.ir wrote:

hi. i have tpr file and cpt file but when i want doing restart for
simulation with,gmx mdrun -s file.tpr -cpi file.cpt command

I'm having trouble. please guide me


With what? You need to be specific about the problem you're having in 
order to get help. We can't guess.


-Justin

--
==

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

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

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Re: [gmx-users] Umbrella sampling simulation stopped in middle.

[Justin Lemkul]

On 12/4/17 1:33 AM, Sailesh Bataju wrote:

Hi,

I've started to pull a dimer of isobutane molecules as a production md
after npt equilibriation. Here is the md_pull.mdp file for production md.

; Umbrella pulling, production md
; preprocessing parameters
title  = Umbrella Sampling
; run parameters
integrator = md ; leap-frog integrator for integrating Newton's equations
of motion
nsteps = 100 ; 10^6 steps to integrate or maximize i.e. total =
5*10^5*1x10^-15 = 0.5 ns
dt = 0.001 ; time step for integration i.e. 1fs=0.001ps
nstcomm = 100 ; frequency for center of mass motion removal
; output control parameters
nstxout = 1000 ; save coordinates every 1000*1x10^-15 = 1ps
nstvout = 1000 ; save velocities every 1ps
nstenergy = 1000 ; save energies every 1ps
nstfout = 1000 ; number of steps that elapse between writing forces to
output trajectory
nstlog = 1000 ; update log file every 1ps
nstxtcout = 1000 ; gives 1000 frames for umbrella sampling generates .xtc
file
energygrps = Alkane SOL ; groups of the molecules present in the system
that writes to the energy file
; neighbour searching parameters
cutoff-scheme = verlet
nstlist = 10 ; frequency to update neighbour list
ns_type = grid ; search neighboring grid cells
rlist = 1.0 ; Cut-off distance for the short-range neighbor list
pbc = xyz ; periodic boundary conditions in all directions
; electrostatics, vdw and ewald parameters
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 4 ; Interpolation order for PME. 4 equals cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
rcoulomb = 1.0 ; distance for coulomb cut-off
epsilon-r = 1.0 ; relative dielectric constant
rvdw = 1.0 ; distance for the LJ or Buckingham cut-off (short-range van der
waal's cut-off)
optimize_fft = yes
; temperature coupling in on
tcoupl = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Alkane SOL ; groups to couple separately to temperature bath
tau-t = 0.2 0.2 ; time constant for coupling
ref-t = 298 298 ; according to experiment performed before
ld-seed = 1225 ; random seed for temperature
; pressure coupling is on
pcoupl = Parrinello-Rahman ; The box is scaled every timestep,Exponential
relaxation pressure coupling with time constant tau-p
pcoupltype = isotropic
tau-p = 1 ; time constant for coupling in ps
compressibility = 4.6e-5 ; For water at 1 atm at 300K is 4.6e-6bar^(-1)
ref-p = 1 ; reference pressure
refcoord-scaling = com
DispCorr = EnerPres ; apply long range dispersion corrections for Energy
and Pressure
; generate velocity at 298K
gen-vel = no ; generate velocity initially
gen-temp = 298 ; generate temperature for Maxwell distrAlkanetion
gen-seed = 12345 ; given seed
; bonds parameters
continuation = yes ; continue after npt
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
constraint-algorithm = LINCS ; LINear Constraint Solver, holonomic
constraints
; pull code
pull  = yes
pull_coord1_type = umbrella ; Center of mass pulling using an umbrella
potential between the reference group and one or more groups.
pull-ngroups = 2  ; there are two groups that are subject to a biasing
potential
pull-group1-name = IBU_IBU_1 ; The name of the pull group, is looked up in
the index file
pull-group2-name = IBU_IBU_2
pull-coord1-geometry = distance ; pull along the vector connecting the two
groups
pull-ncoords = 1 ; The number of pull coordinates
pull-coord1-groups = 1 2 ; groups 1 and 2 (designated by name above as CA
and CB, respectively) define the reaction coordinate
pull-coord1-k = 840 ; The force constant. For umbrella pulling this is the
harmonic force constant in [kJ mol-1 nm-2]
; 2kcal mol^-1 angostrom^-2 = 840 kJ/mol/nm^2 according to paper
pull-coord1-rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull-coord1-dim = Y Y Y ; pulling in all x,y and z direction
pull-coord1-start = yes ; use whatever the distances in the coordinate file
are.

It generated 1000 configuration files without any error. With a separation
of windows of 0.05 nm, i've generated about 23 frames for automated
simulation using python script. All frames went good but last 4 frames
produce error like this:-

Program gmx mdrun, VERSION 5.1.4
Source code file:
/home/akash/Downloads/gromacs-5.1.4/src/gromacs/pulling/pull.cpp,
line: 520

Fatal error:
Distance between pull groups 1 and 2 (1.683443 nm) is larger than 0.49
times the box size (1.717592).
You might want to consider using "pull-geometry = direction-periodic"
instead.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I think this error has to warn us during production md so that future
simulation runs well. Should I change pull-geometry = direction-periodic
(from distance) to continue simulation? If I do so for the remaining 4
frames, does it produce different results (relative to pull-geometry =
distance)? I've no idea what is the best to be done for the last 4 frames.
Considering the time I spent for 

Re: [gmx-users] how to creat new.rtp for acetylated lysine (ALY)

[Justin Lemkul]

On 12/4/17 5:27 AM, Mehreen Jan wrote:

HI!
Hope you all will be fine.
Version : Gromacs5.1.4
Thank you for your reply. According to your advice I have pasted parameters for 
acetylated lysine (ALY) from “stream/prot/toppar_all36_prot_modify_res.str 
(RESI ALY)” in the Charmm36ff (merged.rtp). As you suggested that just create a 
new .rtp entry based on LYS and add it to residuetypes.dat.  Can we rename 
merged.rtp with new .rtp? How to create new.rtp? Can we add ALY as protein in   
residuetypes.dat?   When we past ALY parameters in merged.rtp gives the 
following error
 :at line ALY 
error *.
I have removed these asterisk (*) but it gives the following error:
 : in .rtp file in residue 
ALY at line
   : Atom N NH1 -0.47 !.
Would you like to please tell me how these parameters should be integrated in 
any force field or in Charmm36 that


You can't simply copy and paste from a CHARMM RTF into a GROMACS .rtp 
file and expect it to work. The format is entirely different.


Look at standard LYS and see how it is formatted. Copy its entry, modify 
as needed, and keep it in the same .rtp file (no need for more .rtp 
files, just write a new residue entry in the existing file).


-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] Problem with topology generation by Amber 12 ff

[Justin Lemkul]

On 12/4/17 1:45 AM, Amir Zeb wrote:

Hello gmx users,

I have generated topology and coordinate files of ZN metalloprotein by
Amber 12 ff. Now I am facing this following issue at grompp run:

"ERROR 1 [file topol_Protein_chain_A.itp, line 49741]:
   No default Improper Dih. types"

If I use another ff like Amber99SB- ILDN, there is no such error. I
searched out the solution on google but could not find the answer.

Please help me how to fix this issue?


Which atoms are in that interaction on that line, and should there be 
such an interaction 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] Conversion of charmm36 parameters from namd to gromacs

[Justin Lemkul]

On 12/4/17 7:47 AM, Daniel Bauer wrote:

Hello Justin,

Thanks for your response. I was under the assumption that entries in [
pairtypes ] are the ones that override standard LJ interactions derived
by pairgen. I now know this is a different section.

 From what you are saying I come to the conclusion that the POT O
interaction in charmm36 for gromacs have no custom potential but are
derived via combination rules (as they are in namd). Nevertheless, the
numbers still dont seem to match:

Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for
POT-O, the resulting parameters from the namd version are:

sig = 0.3463750 nm; eps=0.42750571533 kJ/mol


Can you please share the source of these parameters? There should be no 
"NAMD version" of anything. The force field files that you should be 
using are just the CHARMM distribution. The GROMACS port of CHARMM36 
comes directly from those files. There is no official NBFIX for POT-O 
(yet, we do have one but it's not in the official distribution) so the 
combination rules should prevail.


-Justin


However, combining the entries for O and POT in the atomtypes section of
the gromacs version i get something different:

[ atomtypes ]
O  815.9990000.000  A  0.302905564168  0.50208
POT1939.0983000.000  A  0.314264522824  0.36401
===

sig = 0.308585043 nm; eps=0.42750689 kJ/mol

Again, the epsilon value is matching the namd version while sigma is
still off by about 0.4 A.

If my conversion of the namd parameters and combination rules are
correct, this would be a problem. The different position of the energy
minimum results in a potential energy difference of around 7 kJ/mol for
a distance of 0.29 nm (typical distance for POT-O in the selectivity
filter of potassium channels, see attached image).
Can you give me a source where I can read up on why the values for sigma
and epsilon in gromacs are the way they are? It must be more than a
direct conversion of the numbers from kcal to kJ. Or did I again made a
mistake or took the wrong numbers?

Best regards,
Daniel



On 12/03/2017 11:23 PM, Justin Lemkul wrote:


On 12/3/17 4:18 PM, Daniel Bauer wrote:

Hello,


I compared the LJ parameters for the interaction Potassium - backbone
carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
forcefield. I found different numbers for the sigma value i cannot
explain to myself:


The stock charmm36 implementation has the following LJ parameters for
potassium and oxygen:

; atomEmin (kcal/mol)Rmin/2 (A)

POT0.0871.76375

O0.1201.7


Converting the above values to units used in gromacs (kJ/mol and nm) and
applying standard combination rules this should give the following
nonbonded energy parameters:

[ pairtypes]

; sig = (Rmin,i/2 + Rmin,j/2)/10

; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ

; ijfuncsig (nm)eps (kj/mol)

OPOT10.346 0.4275

However, the actual entry for the interaction in GROMACS/charmm36 has
the energy minimum at a much smaller distance (epsilon is on the point
though!)

; ij func sig (nm)eps (kJ/mol)

OPOT10.2820.4275


Can somebody tell me the reason for this huge difference? Is there an
error in my calculation? I am trying to convert an NBFIX applied to this
specific interaction to gromacs. However, I am not sure how to proceed
without doing the reparametrization in gromacs again, because the stock
values differ that much.

This is actually a value that isn't used. [pairtypes] are for 1-4
interactions, which can never occur between a K+ ion and a carbonyl O.
The inclusion in the list is just because it's really hard to tell our
conversion program to exclude some massive list of impossible
interactions. So they get generated.

But to your point, you're missing a critical point of the CHARMM
parameter format. The full NONBonded parameter entry in
par_all36m_prot.prm for carbonyl O is:

O  0.00  -0.12 1.70   0.00  -0.12 1.40

The last fields are epsilon and Rmin/2 when that atom type is used in
a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded
interaction, -0.12/1.4 is for any 1-4 involving O.

-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] Usage of GROMACS

[Smith, Micholas D.]

Hi Momin,

Unfortunately, crystalline structures are, as you have experienced, not the 
easiest thing to simulate using gromac's system building tools. Typically, 
people working on MOFs, clays, general polymers, and other non-biological 
systems use something like LAMMPS (or DL_Poly like you have already noted). 
That being said, it isn't impossible to use gromacs for these types of systems, 
it just takes a bit of time. 

One tool that can be useful for these types of systems with gromacs, however, 
is the x2top tool. It is far from perfect, but it can get you started in the 
right direction.

-Micholas

===
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 Momin Ahmad 

Sent: Monday, December 04, 2017 8:27 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Usage of GROMACS

Hello,

is GROMACS meant to be used for simulations of crystaline structures
(Metal Organic Frameworks, porous materials, minerals, ...)? Almost
every paper working on MD simulations with said structures use DL_Poly
or other software. So my question would be is there a community that
uses GROMACS to simulate crystaline structures? Porting .cif files to
pdb and then trying to run pdb2gmx with writing a .rtp file is very time
consuming.

Cheers
Momin

--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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[gmx-users] Usage of GROMACS

[Momin Ahmad]

Hello,

is GROMACS meant to be used for simulations of crystaline structures 
(Metal Organic Frameworks, porous materials, minerals, ...)? Almost 
every paper working on MD simulations with said structures use DL_Poly 
or other software. So my question would be is there a community that 
uses GROMACS to simulate crystaline structures? Porting .cif files to 
pdb and then trying to run pdb2gmx with writing a .rtp file is very time 
consuming.


Cheers
Momin

--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Daniel Bauer]

Hello Justin,

Thanks for your response. I was under the assumption that entries in [
pairtypes ] are the ones that override standard LJ interactions derived
by pairgen. I now know this is a different section.

From what you are saying I come to the conclusion that the POT O
interaction in charmm36 for gromacs have no custom potential but are
derived via combination rules (as they are in namd). Nevertheless, the
numbers still dont seem to match:

Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for
POT-O, the resulting parameters from the namd version are:

sig = 0.3463750 nm; eps=0.42750571533 kJ/mol

However, combining the entries for O and POT in the atomtypes section of
the gromacs version i get something different:

[ atomtypes ]
O  815.9990000.000  A  0.302905564168  0.50208
POT1939.0983000.000  A  0.314264522824  0.36401
===

sig = 0.308585043 nm; eps=0.42750689 kJ/mol

Again, the epsilon value is matching the namd version while sigma is
still off by about 0.4 A.

If my conversion of the namd parameters and combination rules are
correct, this would be a problem. The different position of the energy
minimum results in a potential energy difference of around 7 kJ/mol for
a distance of 0.29 nm (typical distance for POT-O in the selectivity
filter of potassium channels, see attached image).
Can you give me a source where I can read up on why the values for sigma
and epsilon in gromacs are the way they are? It must be more than a
direct conversion of the numbers from kcal to kJ. Or did I again made a
mistake or took the wrong numbers?

Best regards,
Daniel



On 12/03/2017 11:23 PM, Justin Lemkul wrote:
>
>
> On 12/3/17 4:18 PM, Daniel Bauer wrote:
>> Hello,
>>
>>
>> I compared the LJ parameters for the interaction Potassium - backbone
>> carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
>> forcefield. I found different numbers for the sigma value i cannot
>> explain to myself:
>>
>>
>> The stock charmm36 implementation has the following LJ parameters for
>> potassium and oxygen:
>>
>> ; atomEmin (kcal/mol)Rmin/2 (A)
>>
>> POT0.0871.76375
>>
>> O0.1201.7
>>
>>
>> Converting the above values to units used in gromacs (kJ/mol and nm) and
>> applying standard combination rules this should give the following
>> nonbonded energy parameters:
>>
>> [ pairtypes]
>>
>> ; sig = (Rmin,i/2 + Rmin,j/2)/10
>>
>> ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ
>>
>> ; ijfuncsig (nm)eps (kj/mol)
>>
>> OPOT10.346 0.4275
>>
>> However, the actual entry for the interaction in GROMACS/charmm36 has
>> the energy minimum at a much smaller distance (epsilon is on the point
>> though!)
>>
>> ; ij func sig (nm)eps (kJ/mol)
>>
>> OPOT10.2820.4275
>>
>>
>> Can somebody tell me the reason for this huge difference? Is there an
>> error in my calculation? I am trying to convert an NBFIX applied to this
>> specific interaction to gromacs. However, I am not sure how to proceed
>> without doing the reparametrization in gromacs again, because the stock
>> values differ that much.
>
> This is actually a value that isn't used. [pairtypes] are for 1-4
> interactions, which can never occur between a K+ ion and a carbonyl O.
> The inclusion in the list is just because it's really hard to tell our
> conversion program to exclude some massive list of impossible
> interactions. So they get generated.
>
> But to your point, you're missing a critical point of the CHARMM
> parameter format. The full NONBonded parameter entry in
> par_all36m_prot.prm for carbonyl O is:
>
> O  0.00  -0.12 1.70   0.00  -0.12 1.40
>
> The last fields are epsilon and Rmin/2 when that atom type is used in
> a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded
> interaction, -0.12/1.4 is for any 1-4 involving O.
>
> -Justin
>

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.

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Re: [gmx-users] Metal-Protein interactions

[RAHUL SURESH]

Dear Justin

I have manually added Cu ion to the protein structure. the total charge of
the system is -0.9. How do I make sure that  gromacs is considering Cu
in +2 state only?

thank you

On Wed, Nov 29, 2017 at 4:33 PM, RAHUL SURESH 
wrote:

> Thank you Justin.
>
> It was helpful
>
> On Wed, Nov 29, 2017 at 7:33 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/28/17 1:00 PM, RAHUL SURESH wrote:
>>
>>> On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul  wrote:
>>>
>>>
 On 11/28/17 4:54 AM, RAHUL SURESH wrote:

> I am trying to simulate a metal-protein interaction using gromacs 2016
> package and charmm36 ff.
> I have prepared the initial pdb by performing an oniom calculations
>
 between

> protein and metal (at various positions) using gaussian 09 and chose
> the
> structure with maximum binding energy. The metal ion is bonded to
> oxygen
> atom of His residue. Having a look at gro file after each step
>
 That's unusual; His typically coordinate metals via their delta or
 epsilon N atoms.

 Sorry that I pronounced wrongly as oxygen.. regret the inconvenience.
>>>
>>> (protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
> and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over
> the
> course of simulations for 10ns, the metal ion is away from the protein.
>
> What can be done to have the metal ion restrained at its position? Or
> if
>
 I

> extend the simulation will the metal ion find its appropritae position
> during the course time?
>
 Unlikely. This is a fundamental issue with classical mechanical force
 fields approximating ion interactions very poorly, particularly in the
 case of multivalent and/or transition metals. There are many effects
 like polarization and charge transfer that simply can't be modeled. You
 can apply distance restraints (or actual covalent bonds), NBFIX LJ
 parameters, etc.

>>> while restraing the metal ion, it arise an error stating that an atom can
>>> not be mentioned in two groups.
>>> Tc grps = protein_cu water_and_ions.
>>> Cu will already be mentioned in ions.
>>>
>>
>> It should be grouped with the protein; a coordinated metal is
>> functionally part of the protein and should be treated as such. It makes no
>> sense to couple it to the solvent thermostat.
>>
>> and that may be enough to preserve the binding pose. In
>>>
 reality, one would have to reparametrize any ligating residues because
 the charge distribution on the ion and anything coordinating it is not
 at all what the standard force field uses.

>>> Reparameterize.? Means I have to add additional parameter file to the
>>> charmm36 ff after interacting with metal ion.?
>>>
>>
>> It means you would have to derive new residue definitions, but a QM/MM
>> approach is probably superior.
>>
>>
>>> Also Justin, what if I can manually add a bond between N of HIS and metal
>>> ion with most appropriate bond length ..?
>>> (To avoid complexity if it works)
>>>
>>
>> Yes, that is a possibility, but again you will have to do some QM work to
>> properly parametrize the geometries and vibrational frequencies for the new
>> bonded parameters (which then include angles and dihedrals). Cu2+ is a
>> difficult ion to deal with, though, so this may be surprisingly laborious.
>>
>>
>> -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
>>
>> ==
>>
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>



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*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Topology file of molecule

[Krzysztof Kolman]

Dear Justin,

Since you last answer, I have been trying to find some description how to
perform dihedrals scans using some QM software and Gromacs. I have found
out that it used to be some QM software implemented in Gromacs (Orca) but
this implementation is not developed anymore and it does not work with
newer version of Gromacs and Orca, please correct me here if I am wrong. I
have been also trying to find out how to do the MM part using Gromacs and I
found out that the simulations should have some unusual  parameters
(cutoffs, etc.) and it is quite tedious work since all the input files need
to be manually prepared. My question is do you know maybe if there is
somewhere a tutorial how to perform such scans using Gromacs where all this
knowledge is combined and also some semi-automatic solution is presented?

Best regards,
Krzysztof

2017-11-23 13:55 GMT+01:00 Justin Lemkul :

>
>
> On 11/23/17 7:51 AM, Magnus Lundborg wrote:
>
>> Dear Krzysztof,
>>
>> I wouldn't be too worried about the fact that GAFF parameters have been
>> used for proper and improper torsion angles. It happens quite a lot with
>> the OPLS-AA forcefield. But as always, it is good to verify that the
>> topology behaves as expected. Unfortunately there is no objective way to do
>> this. If there are no experimentally measured properties available of your
>> molecule it is a bit risky to proceed. However, I would recommend running
>> short simulations of the molecule in vacuum (NVT) and in a simulation box
>> solvated by itself just to see that it does at least not behave very
>> strangely. If it seems OK I think you can proceed with your studies, but as
>> always with an eye open for strange behaviour.
>>
>>
> The rigorous test is to perform a QM energy scan over the dihedral. Rotate
> in increments of 15 degrees, optimize, and calculate the energy. This gives
> you a one-dimensional potential energy surface. Do the corresponding MM
> evaluations with the force field (in vacuo) and verify that the positions
> and magnitudes of the minima are comparable. If they're not, you need to do
> some refinement of the parameters. Otherwise it is extremely hard to define
> what "strange" is in a simulation; you don't know what the molecule should
> be doing in the first place.
>
> -Justin
>
>
> I hope that helps you.
>>
>> Best regards,
>>
>> Magnus
>>
>> On 2017-11-23 10:24, Krzysztof Kolman wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I would like to perform a simulation of adsorption of
>>> 3,4-Dihydroxybenzoic
>>> acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created
>>> topology files for the silica surface based on the information found in
>>> papers describing simulations of quartz (Wensink 2000
>>> - 10.1021/la053284f, van der Spoel 2006 -10.1021/la053284f ). The
>>> topology
>>> for 34DHBA was created using STaGE script (Lundborg 2015
>>> - 10.1021/jp505332p) but some of the parameters (dihedrals) were missing
>>> and GAFF parameters were used instead. Please find below the content of
>>> itp
>>> file:
>>>
>>> [ moleculetype ]
>>> ; Namenrexcl
>>>   34DHBA_opls 3
>>>
>>> [ atoms ]
>>> ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
>>>   bond_type
>>>1opls_145 1   LIG   C11 -0.115000   12.01100 ; -0.115000
>>>   CA
>>>2opls_166 1   LIG   C22  0.15   12.01100 ; 0.035000
>>>   CA
>>>3opls_166 1   LIG   C33  0.15   12.01100 ; 0.185000
>>>   CA
>>>4opls_145 1   LIG   C44 -0.115000   12.01100 ; 0.07
>>>   CA
>>>5opls_145 1   LIG   C55 -0.115000   12.01100 ; -0.045000
>>>   CA
>>>6opls_145 1   LIG   C66 -0.115000   12.01100 ; -0.16
>>>   CA
>>>7opls_167 1   LIG   OC3   7 -0.585000   15.99940 ; -0.745000
>>>   OH
>>>8opls_167 1   LIG   OC2   8 -0.585000   15.99940 ; -1.33
>>>   OH
>>>9opls_470 1   LIG   C99  0.635000   12.01100 ; -0.695000
>>>   C
>>>10   opls_269 1   LIG   OC91  10-0.44   15.99940 ; -1.135000
>>>   O_3
>>>11   opls_268 1   LIG   OC92  11-0.53   15.99940 ; -1.665000
>>>   OH
>>>12   opls_146 1   LIG   HC1   12 0.1150001.00800 ; -1.55
>>>   HA
>>>13   opls_146 1   LIG   HC4   13 0.1150001.00800 ; -1.435000
>>>   HA
>>>14   opls_146 1   LIG   HC6   14 0.1150001.00800 ; -1.32
>>>   HA
>>>15   opls_168 1   LIG   HO3   15 0.4350001.00800 ; -0.885000
>>>   HO
>>>16   opls_168 1   LIG   HO2   16 0.4350001.00800 ; -0.45
>>>   HO
>>>17   opls_270 1   LIG   HO92  17 0.451.00800 ; 0.00
>>>   HO
>>>
>>> [ bonds ]
>>> ;   ai aj funct   r k
>>>  1   2   1   1.4000e-01   3.9246e+05 ; CA - CA
>>>  1   6   1   1.4000e-01   3.9246e+05 ; CA - CA
>>>  1   12   1   1.0800e-01   3.0711e+05 ; CA - HA
>>>  2   3   1   1.4000e-01   3.9246e+05 ; CA - CA
>>>  2   8   1   1.3640e-01   

[gmx-users] how to creat new.rtp for acetylated lysine (ALY)

[Mehreen Jan]

HI!
Hope you all will be fine.
Version : Gromacs5.1.4
Thank you for your reply. According to your advice I have pasted parameters for 
acetylated lysine (ALY) from “stream/prot/toppar_all36_prot_modify_res.str 
(RESI ALY)” in the Charmm36ff (merged.rtp). As you suggested that just create a 
new .rtp entry based on LYS and add it to residuetypes.dat.  Can we rename 
merged.rtp with new .rtp? How to create new.rtp? Can we add ALY as protein in   
residuetypes.dat?   When we past ALY parameters in merged.rtp gives the 
following error 
:at line ALY 
error *.
I have removed these asterisk (*) but it gives the following error:
: in .rtp file in residue 
ALY at line
  : Atom N NH1 -0.47 !.
Would you like to please tell me how these parameters should be integrated in 
any force field or in Charmm36 that it works smoothly.
Thank you 
Mehreen Gul
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Re: [gmx-users] force field packages

[Mark Abraham]

Hi,

Thanks for the tip, I brought the website back up. Most of the relevant
force fields are in the repo, however.

Mark

On Mon, Dec 4, 2017 at 7:54 PM Zahedeh Bashardanesh 
wrote:

> Hi,
>
> Does anybody know where else to get the reliable amber force field package
> for gromacs except from gromacs website? The webpage has been down since
> Saturday.
>
> Best,
>
> ---
> Zahedeh Bashardanesh, Ph.D. Candidate
> Department of Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden
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[gmx-users] force field packages

[Zahedeh Bashardanesh]

Hi,

Does anybody know where else to get the reliable amber force field package
for gromacs except from gromacs website? The webpage has been down since
Saturday.

Best,
---
Zahedeh Bashardanesh, Ph.D. Candidate
Department of Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden
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