Re: [gmx-users] simulation at different temperature

[Alex Mathew]

Dear Justin,
Thanks for the reply, Could you tell me what is the unique purpose of the
REMD and where I can learn it from basics?
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 24

[amitabh jayaswal]

... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm
repeatedly getting.
Please rectify/improve.
Thanks and regards!

*Amitabh Jayaswal*
*PhD Bioinformatics Scholar*
*Banaras Hindu University*
*Varanasi, U.P., India | PIN-221005*
  *+*
*City Coordinator*
*United Nations*
*Rio+22 Power India Program*
M: +91 (9868 330088 and 7376 019 155)


On Thu, Jul 6, 2017 at 12:21 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
>
> Today's Topics:
>
>1. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 165
>   (Davide Bonanni)
>2.  Charge Mutation (State B) for Ions (Hermann, Johannes)
>3. Number of ions in Anionic lipid system- Charmm-GUI (Nidhin Thomas)
>4. simulation at different temperature (Alex Mathew)
>5. Re: simulation at different temperature (Alex)
>6. Re: simulation at different temperature (Alex Mathew)
>
>
> --
>
> Message: 1
> Date: Wed, 5 Jul 2017 17:09:14 +0200
> From: Davide Bonanni 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue
> 165
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Hannes,
>
> Thank you very much for your reply, really appreciated.
>
>
>
> > Date: Mon, 26 Jun 2017 12:09:45 +0100
> > From: Hannes Loeffler 
> > To: 
> > Cc: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> > Message-ID: <20170626120945.75215...@stfc.ac.uk>
> > Content-Type: text/plain; charset="US-ASCII"
> >
> > On Mon, 26 Jun 2017 12:25:19 +0200
> > Davide Bonanni  wrote:
> >
> > > 1) Can I perform the calculation in a single step with soft core
> > > potential enabled? I mean, is it correct to transform directly the
> > > hydrogen into a chlorine instead of using 2 topologys and 2
> > > complexes, where in the first step I transform the hydrogen into
> > > dummy atom, and in the second I transform the dummy atom into
> > > chlorine.
> >
> > Technically speaking you can perfectly do that but in practice it can
> > be much more efficient to directly and linearly transform one atom type
> > into another (single topology approach).  There is no need for a
> > softcore potential in this case.  Those would only be activated for
> > atoms that either appear or disappear i.e. atoms with zero vdW
> > parameters.  The input and topology files from FEsetup should be all
> > you need.
>
>
> Can I have problems if I keep active the softcore potential whether is not
> needed?
>
>
> > > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> > > x-tutorials/free_energy/index.html), I have to perform every step of
> > > molecular dynamics at every Lambda value, is that right?
> >
> > Yes, you will need to do a simulation for every and each lambda step.
> >
> >
> > > 3) I run a test minimization step (mdp file attached) of my complex
> > > at the last "init-lambda-state", 15 in my case. Looking at the .trr
> > > output file I can see that the bond between the carbon and the
> > > hydrogen which should be trasformed is longer than a normal C-H bond,
> > > but the atom is still recognized as hydrogen (picture
> > > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> > > blue -> init-lambda-state = 15). I was wondering if this is what I am
> > > supposed to see, so if gromacs is considering the state B of my
> > > system where I have chlorine bound to carbon instead hydrogen.
> >
> > What does "recognized as hydrogen" mean?  I suspect that what you are
> > referring to is the output of some visualisation program because you
> > instructed it to interpret that particular atom to be a hydrogen.
> >
> > What you need to expect to see is that a C-H bond is transformed into a
> > C-Cl bond and accordingly the bond length increases.
> >
>
> Of course, It's like you said. I see the bond length to increase as in the
> img "http://tinypic.com/r/2wp11dh/9;.
> Thank you again.
>
> Cheers,
>
> Davide Bonanni
>
>
> 

Re: [gmx-users] simulation at different temperature

[Alex]

Sure, and I suggested that alternative.

Alex

On Wed, Jul 5, 2017 at 3:45 PM, Justin Lemkul  wrote:

>
>
> On 7/5/17 3:09 PM, Alex wrote:
>
>> I don't understand the objection. This _is_ full dynamics of the system
>> containing behavior at all desired temperatures.
>> After it's done, you can easily split trajectories into the desired
>> annealing regions. Alternatively, you could simply script this as a
>> sequence of separate runs based on mdp's with gradually increasing T,
>> simply throw away a few first ns of each simulation before analyzing.
>>
>>
> I don't see the benefit of annealing.  A big challenge (with any
> simulation) is sampling, and a single run of increasing temperature leaves
> you waiting for a long time (because you need sufficient time at each
> temperature) and you still only have one run.  If all one cares about is
> temperature dependence of dynamics, I'd just simulate N replicates at each
> temperature, independently, and acquire data in a much more efficient
> manner.
>
> -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
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Re: [gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

[Justin Lemkul]

On 7/5/17 12:17 PM, Nidhin Thomas wrote:

Hi Justin,

Thanks a lot for the prompt reply.

I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM 
KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are 
correct? Could you please tell me how I can check the correct number of ions?



Look at the CHARMM-GUI output, note how it calculates volume, and pull out a 
calculator for moles/volume :)  Neutral lipids require no counterions, so 
everything you add is just the desired salt concentration.



The size of the original system (300 POPC + 100 POPG) was (11.7480468  
11.7480468  8.98 ) nm. If the size of the system is very small to accommodate 
the ions, how can I change the size of the system in charmm-gui ? Or should I 
just get the bilayer system and add ions by myself using gonion command in 
gromacs?



IIRC you can control how many hydrating waters you get per lipid.  If you 
increase the number of waters, this will increase the volume.


-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] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff

[Justin Lemkul]

On 7/5/17 10:47 AM, Sonia Milena Aguilera Segura wrote:

On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote:

Dear GROMACS users,

I am currently interested in studying properties of some solvents, among
them acetonitrile and isopropanol. I would like to use CHARMM force field
for compatibility with other molecules and I am taking my initial
structure files from virtualchemistry.org. Does someone know how to run
the 6-sites model available with the CHARMM ff in gromacs? As I try to run
the simulation box I get the error "No Defaul Proper Dih. Types". I
checked the ffbonded file and I didn't see the dihedrals defined as in the
rtp file. And for what I've understood this is


Dihedrals aren't required in .rtp files since pdb2gmx generates them.



Dear Justin,

Thank you for the comments. Yes, sorry, I was referring to the top file 
generated by pdb2gmx instead of the rtp file. The top file has the dihedrals 
defined whereas ffbonded files does not.




because acetonitrile is a linear molecule and dihedrals for three colinear
atoms
this are mathematically

There are still H-C-C-N dihedral terms.



Yes, they are named in the top file but not really defined in the ffbonded 
file, which is why I get the error.



pdb2gmx will blindly generate all possible dihedrals; sometimes this isn't 
right.

It even appears that such parameters (H-C-C-N) do not exist in any CHARMM force 
field file.  Perhaps it's meant that way, but I have never tried to simulate 
anything with it.






undefined. Also, when I go to check the available itp for acetonitrile in
virtualchemistry.org, I can see that there is a 7-sites model,with a dummy
atom
included. However, for this case, pdb and itp files do not match. I have seen
that this can be sort of solved by fixing the angle as 179.9, but I really
don't
exactly what to change

or where in the force field files. I have no experience modifying force
fields. Also, I've seen that for


Don't modify the force field.  The CHARMM parameters for acetonitrile were
generated in CHARMM, which can handle linear angles without the tricks that
GROMACS requires with virtual sites.



So, what you are saying is that it is not possible to simulate the 6-sites 
model of acetonitrile in GROMACS using CHARMM?


Never tried it.  AFAIK, GROMACS needs special treatment for linear species. 
Hopefully someone who has actually done such a simulation will say something, 
because my usefulness here is at its end :)


-Justin





the opls ff both pdb and itp files match, but I really need to use the CHARMM
force field. Are the opls parameters compatible with CHARMM? Any advice?




Don't mix and match force fields.



Then, if I cannot run the 6-sites model, what's the advice? I would really need 
to run acetonitrile with CHARMM, because I have other series of molecules such 
as cellulose and other saccharides. In that case, what would be the most 
compatible for field to simulate organic solvents and saccharides?




Also, I cannot find an already optimized structure with all hydrogens for
isopropanol. Could somenone provide one?


Take any valine side chain and use it.  You can generate any missing H easily
with a suitable .hdb entry.

-Justin


Thank you for your advice,

Sonia Aguilera
PhD student
ENSCM



--
==

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] simulation at different temperature

[Justin Lemkul]

On 7/5/17 3:09 PM, Alex wrote:

I don't understand the objection. This _is_ full dynamics of the system
containing behavior at all desired temperatures.
After it's done, you can easily split trajectories into the desired
annealing regions. Alternatively, you could simply script this as a
sequence of separate runs based on mdp's with gradually increasing T,
simply throw away a few first ns of each simulation before analyzing.



I don't see the benefit of annealing.  A big challenge (with any simulation) is 
sampling, and a single run of increasing temperature leaves you waiting for a 
long time (because you need sufficient time at each temperature) and you still 
only have one run.  If all one cares about is temperature dependence of 
dynamics, I'd just simulate N replicates at each temperature, independently, and 
acquire data in a much more efficient manner.


-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] TIP4P/ice pdb file

[Christopher Neale]

I believe that you can use any 4-point water model .gro for any 4-point water 
topology (or likewise for 3-point water models). Did you try it yet? If so, 
what problem are you running into specifically?


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

Sent: 05 July 2017 14:57:26
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] TIP4P/ice pdb file

Dear All,

I would like to simulate water using TIP4P/ice potential. My question is
that how can I generate .gro file for this simulation?
I will use TIP4P/ice topology that is available in SklogWiki, but I cannot
understand how can I generate .gro file for this topology. Can I easily use
TIP4P.gro that is available in share/top? If yes, how can I modify
TIP4P.gro file to use with TIP4P/ice potential?

Best regards,
Golnaz
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[gmx-users] TIP4P/ice pdb file

[G R]

Dear All,

I would like to simulate water using TIP4P/ice potential. My question is
that how can I generate .gro file for this simulation?
I will use TIP4P/ice topology that is available in SklogWiki, but I cannot
understand how can I generate .gro file for this topology. Can I easily use
TIP4P.gro that is available in share/top? If yes, how can I modify
TIP4P.gro file to use with TIP4P/ice potential?

Best regards,
Golnaz
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Re: [gmx-users] simulation at different temperature

[Alex Mathew]

Dear Alex,

I guess this is annealing and which will give only one output.xtc, I'm
looking for full dynamics of the system (say 100 ns for each temperature,
300 K,305 K340 K ). Further, I need to compare the results with each
other.

Thank you.
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Re: [gmx-users] simulation at different temperature

[Alex]

Of course: http://manual.gromacs.org/online/mdp_opt.html -- see 
'simulated annealing'.


Alex


On 7/5/2017 11:45 AM, Alex Mathew wrote:

Dear gmx users,

I would like to see the temperature dependence of an ion channel/membrane
protein in lipid bilayer system. My plan is to run a simulation at 300 K to
340 K by increasing 5 K and observing the permeation of molecules, pore
diameter, sec structure .etc.   Are there any techniques available to do
this at a time? Or I have to run the independent simulation for all these?


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[gmx-users] simulation at different temperature

[Alex Mathew]

Dear gmx users,

I would like to see the temperature dependence of an ion channel/membrane
protein in lipid bilayer system. My plan is to run a simulation at 300 K to
340 K by increasing 5 K and observing the permeation of molecules, pore
diameter, sec structure .etc.   Are there any techniques available to do
this at a time? Or I have to run the independent simulation for all these?
-- 
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[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

[Nidhin Thomas]

Hi Justin,

Thanks a lot for the prompt reply.

I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM 
KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are 
correct? Could you please tell me how I can check the correct number of ions?

The size of the original system (300 POPC + 100 POPG) was (11.7480468  
11.7480468  8.98 ) nm. If the size of the system is very small to accommodate 
the ions, how can I change the size of the system in charmm-gui ? Or should I 
just get the bilayer system and add ions by myself using gonion command in 
gromacs?

Thanks,

Nidhin Thomas

>> Dear GROMACS Users,
>> 
>> I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI.
>> I want to include 0.150 M KCl in the system. When I use the option in 
>> charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the 
>> number of ions using the size of simulation box, I am getting 98 ions.
>> 
>> Can anyone tell me what I should do to get the exact number of ions in the 
>> system?
>> 
> 
> CHARMM-GUI calculates an excluded volume due to the solute (protein, nucleic 
> acid, lipids, etc) so using the total box volume is incorrect when 
> calculating 
> the number of ions in solution.  The result you're getting tells you that 
> your 
> box is too small (insufficient solvent volume) to achieve 150 mM KCl.
> 
>> Would it be correct if I first neutralize the system using 100 K+ ions and 
>> then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system?
>> 
> 
> No, because then your effective concentration is much higher than what you 
> want.
> 
> -Justin
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[gmx-users] Charge Mutation (State B) for Ions

[Hermann, Johannes]

Dear all,

I am doing a FEC via alchemical transformation. In order to keep the 
charge constant I plan to mutate ions at the same time. In particular, I 
want to change the charge of MG ions. My question is did I manipulate 
the .top .itp and .gro file in the right way:


In the topology.top file I added:

#include "topol_MG_Hybrid.itp"

in the beginning and included in the [molecules] section

MG_HBRID26

at the place where my hybrid MGs begin in the .gro file. In the .tip 
file I defined the new moleculetype and the atom:


[ moleculetype ]
; Namenrexcl
MG_HBRID 1
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass 
typeBchargeB  massB
   1   MG1MGXMGHBR  1  2 24.305   
MG   2.30769  24.305


In the gro file I changed the (formaly regular) MGs to:

8702MGX  MGHBR55183  -1.480   0.077   2.991

I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran 
grompp and it compiles without errors. However, I want to make sure, 
that this is consistent with gromacs files and that I will change the 
charge in the simulation.


Thank you very much for your help!

All the best
Johannes


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

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 165

[Davide Bonanni]

Dear Hannes,

Thank you very much for your reply, really appreciated.



> Date: Mon, 26 Jun 2017 12:09:45 +0100
> From: Hannes Loeffler 
> To: 
> Cc: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> Message-ID: <20170626120945.75215...@stfc.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Mon, 26 Jun 2017 12:25:19 +0200
> Davide Bonanni  wrote:
>
> > 1) Can I perform the calculation in a single step with soft core
> > potential enabled? I mean, is it correct to transform directly the
> > hydrogen into a chlorine instead of using 2 topologys and 2
> > complexes, where in the first step I transform the hydrogen into
> > dummy atom, and in the second I transform the dummy atom into
> > chlorine.
>
> Technically speaking you can perfectly do that but in practice it can
> be much more efficient to directly and linearly transform one atom type
> into another (single topology approach).  There is no need for a
> softcore potential in this case.  Those would only be activated for
> atoms that either appear or disappear i.e. atoms with zero vdW
> parameters.  The input and topology files from FEsetup should be all
> you need.


Can I have problems if I keep active the softcore potential whether is not
needed?


> > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> > x-tutorials/free_energy/index.html), I have to perform every step of
> > molecular dynamics at every Lambda value, is that right?
>
> Yes, you will need to do a simulation for every and each lambda step.
>
>
> > 3) I run a test minimization step (mdp file attached) of my complex
> > at the last "init-lambda-state", 15 in my case. Looking at the .trr
> > output file I can see that the bond between the carbon and the
> > hydrogen which should be trasformed is longer than a normal C-H bond,
> > but the atom is still recognized as hydrogen (picture
> > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> > blue -> init-lambda-state = 15). I was wondering if this is what I am
> > supposed to see, so if gromacs is considering the state B of my
> > system where I have chlorine bound to carbon instead hydrogen.
>
> What does "recognized as hydrogen" mean?  I suspect that what you are
> referring to is the output of some visualisation program because you
> instructed it to interpret that particular atom to be a hydrogen.
>
> What you need to expect to see is that a C-H bond is transformed into a
> C-Cl bond and accordingly the bond length increases.
>

Of course, It's like you said. I see the bond length to increase as in the
img "http://tinypic.com/r/2wp11dh/9;.
Thank you again.

Cheers,

Davide Bonanni
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Re: [gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff

[Sonia Milena Aguilera Segura]

> On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote:
> > Dear GROMACS users,
> > 
> > I am currently interested in studying properties of some solvents, among
> > them acetonitrile and isopropanol. I would like to use CHARMM force field
> > for compatibility with other molecules and I am taking my initial
> > structure files from virtualchemistry.org. Does someone know how to run
> > the 6-sites model available with the CHARMM ff in gromacs? As I try to run
> > the simulation box I get the error "No Defaul Proper Dih. Types". I
> > checked the ffbonded file and I didn't see the dihedrals defined as in the
> > rtp file. And for what I've understood this is
> 
> Dihedrals aren't required in .rtp files since pdb2gmx generates them.


Dear Justin, 

Thank you for the comments. Yes, sorry, I was referring to the top file 
generated by pdb2gmx instead of the rtp file. The top file has the dihedrals 
defined whereas ffbonded files does not.  


> 
> because acetonitrile is a linear molecule and dihedrals for three colinear
> atoms
> this are mathematically
> 
> There are still H-C-C-N dihedral terms.


Yes, they are named in the top file but not really defined in the ffbonded 
file, which is why I get the error. 


> 
> undefined. Also, when I go to check the available itp for acetonitrile in
> virtualchemistry.org, I can see that there is a 7-sites model,with a dummy
> atom
> included. However, for this case, pdb and itp files do not match. I have seen
> that this can be sort of solved by fixing the angle as 179.9, but I really
> don't
> exactly what to change
> >or where in the force field files. I have no experience modifying force
> >fields. Also, I've seen that for
> 
> Don't modify the force field.  The CHARMM parameters for acetonitrile were
> generated in CHARMM, which can handle linear angles without the tricks that
> GROMACS requires with virtual sites.


So, what you are saying is that it is not possible to simulate the 6-sites 
model of acetonitrile in GROMACS using CHARMM? 

> 
> the opls ff both pdb and itp files match, but I really need to use the CHARMM
> force field. Are the opls parameters compatible with CHARMM? Any advice?
> > 
> 
> Don't mix and match force fields.


Then, if I cannot run the 6-sites model, what's the advice? I would really need 
to run acetonitrile with CHARMM, because I have other series of molecules such 
as cellulose and other saccharides. In that case, what would be the most 
compatible for field to simulate organic solvents and saccharides?  

> 
> > Also, I cannot find an already optimized structure with all hydrogens for
> > isopropanol. Could somenone provide one?
> 
> Take any valine side chain and use it.  You can generate any missing H easily
> with a suitable .hdb entry.
> 
> -Justin

Thank you for your advice, 

Sonia Aguilera
PhD student
ENSCM
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[gmx-users] EQUILIBRATION

[‪farial tavakoli‬ ‪]

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but 
when I wanted to performance equilibration , i got this ERROR:  
step 1: One or more water molecules can not be settled.
  Check for bad contacts and/or reduce the timestep if 
appropriate

Would you please help me to fix this problem?
These are all stages which I did:
I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands 
and water molecules from it and left just chain A and HETATM ZN A . 
I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx 
-f 4LY1.pdb -o 4LY1.gro -water spc
then made a complex.gro file which include 4LY1.gro and DRG.gro which i got 
from PRODRG site. I also copy paste ; Include ligand topology
#include "DRG.itp"

in the topology file and added DRG as a ligand in [ molecules ] directive. 
Then I defined box by using this command :
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

then defined solvate by :
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

then used grommp to assemble a .tpr file by using a .mdp file and this command :
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

that was my .mdp afile :
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and added 2 CL ions since my total charge was 2.00 because of zn ion. 

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2

then for minimization, i replaced energygroups from system to protein DRG in 
em_real.mdp. that was my em_real.mdp file:

integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol 
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = protein DRG   ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p 
topol.top -o em.tprand
gmx mdrun -v -deffnm em

GROMACS replies:
Steepest Descents converged to Fmax < 1000 in 1833 steps
Potential Energy  = -5.6356275e+05
Maximum force =  9.7815100e+02 on atom 3452
Norm of force =  3.1465845e+01

Simulation ended prematurely, no performance report will be written.
Is there any problem that simulation ended prematurely?

Then for equilibriation i typed gmx genrestr -f jz4.gro -o posre_jz4.itp -fc 
1000 1000 1000

and in order to restrain both the protein and the ligand simultaneously, I 
specify define = -DPOSRES -DPOSRES_LIG in the .mdp file. 
then typed   gmx make_ndx -f em.gro -o index.ndx

to merge the protein and DRG. and selected protein and DRG by :
> 1 | 14
> qthen set tc_grps = Protein_DRG Water_and_ions in NVT.mdp file to achieve my 
> desired "Protein Non-Protein" effect. that was my NVT.mdp file:

title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG 
; position restrain the protein and ligand
integrator = md ; leap-frog integratornsteps = 5 ; 2 * 5 = 100 psdt 

[gmx-users] Hydroxyapatites parameter

[Мижээ Батсайхан]

Dear gmx users,

I would like to simulate hydroxyapatites with biological molecules. How can
I simulate this type of systems using groamcs? Are there any parameters for
hydroxyapatite? Please.

Best regards,
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[gmx-users] the sum of the two largest charge group radii is larger than rlist

[morpheus]

Hi,

I get the following error:

"
Largest charge group radii for Van der Waals: 6.762, 6.758 nm
Largest charge group radii for Coulomb:   9.487, 9.465 nm

WARNING 1 [file md_vsIonDod.mdp]:
  The sum of the two largest charge group radii (18.951988) is larger than
  rlist (1.40)
"

I found this on the gromacs webpage:

"A similar error ("The sum of the two largest charge group radii (X) is
larger than rlist") can arise under two circumstances:

   1. The charge groups are inappropriately large or rlist is set too low.
   2. Molecules are broken across periodic boundaries, which is not a
   problem in a periodic system.  In this case, the sum of the two largest
   charge groups will correspond to a value of twice the box vector along
   which the molecule is broken."


If I visualise my protein with VMD nothing seems to be broken across the
box boundary ... I also tried:

gmx trjconv -s JM22_onlyFullTCR_pbc.pr.pdb -f JM22_onlyFullTCR_pbc.pr.pdb
-o JM22_onlyFullTCR.pr.pdb -pbc whole

... but the warning stays the same - do I have a problem or can I just
ignore the warning?


Thanks!

M
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Re: [gmx-users] Flat-bottom spherical potential

[Justin Lemkul]

On 7/5/17 8:36 AM, Shraddha Parate wrote:

Hello all,

I had emailed to Gromacs Users List the following query as per the attached
thread (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
users/2017-June/114166.html)

Justin mentioned about applying a flat-bottom spherical potential which
will keep the droplet formed on the surface. I tried my best to figure out
the corresponding file to implement the potential, but could not find. Can
anyone please let me know more clearly on how I can make this kind of
changes?



The origin of the potential is at the center of the sphere.  You would apply a 
flat-bottom restraint to the water oxygens by assigning a suitable spherical 
restraint and a radius that you want (see the manual).  Then, you need to 
generate a "fake" coordinate file that sets the (x,y,z) coordinates of each 
water O atom to the center of the sphere and pass this coordinate file to grompp 
-r.  This sets the origin of the restraint, so that the radius you want is enforced.


-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] Acetonitrile and isopropanol with CHARMM ff

[Justin Lemkul]

On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote:

Dear GROMACS users,

I am currently interested in studying properties of some solvents, among them acetonitrile and isopropanol. I would like to use CHARMM force field for compatibility with other molecules and I am taking my initial structure files from virtualchemistry.org. Does someone know how to run the 6-sites model available with the CHARMM ff in gromacs? As I try to run the simulation box I get the error "No Defaul Proper Dih. Types". I checked the ffbonded file and I didn't see the dihedrals defined as in the rtp file. And for what I've understood this is 


Dihedrals aren't required in .rtp files since pdb2gmx generates them.

because acetonitrile is a linear molecule and dihedrals for three colinear atoms 
this are mathematically


There are still H-C-C-N dihedral terms.

undefined. Also, when I go to check the available itp for acetonitrile in 
virtualchemistry.org, I can see that there is a 7-sites model,with a dummy atom 
included. However, for this case, pdb and itp files do not match. I have seen 
that this can be sort of solved by fixing the angle as 179.9, but I really don't 
exactly what to change
   or where in the force field files. I have no experience modifying force fields. Also, I've seen that for 


Don't modify the force field.  The CHARMM parameters for acetonitrile were 
generated in CHARMM, which can handle linear angles without the tricks that 
GROMACS requires with virtual sites.


the opls ff both pdb and itp files match, but I really need to use the CHARMM 
force field. Are the opls parameters compatible with CHARMM? Any advice?




Don't mix and match force fields.


Also, I cannot find an already optimized structure with all hydrogens for 
isopropanol. Could somenone provide one?


Take any valine side chain and use it.  You can generate any missing H easily 
with a suitable .hdb entry.


-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] methylated HSP

[Justin Lemkul]

On 7/4/17 1:32 PM, Emma Ahlstrand wrote:

Hi,

I am going to simulate a protein with a methylated histidine in Gromacs using 
CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in 
pdf file.

I have followed the discussion in 
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=15364=all
but I cannot see that NR3 is the proper atomtype. I have tried to add bonds, 
angles and dihedrals for NR3 and the methyl,:

[ bondtypes ]
;  ij  func   b0   kb
  NR3  CT3 1   0.149 167360.00 ; inserted for methylated 
HIS (HIC)
[ angletypes ]
;  ijk  func   theta0   ktheta  ub0 
 kub
  NR3  CT3  HA3 5   107.50   472.792000   0.
 0.00 ;inserted for HIC
[ dihedraltypes ]
;  ijkl  func phi0 kphi  mult
  NR3 CPH2  NR3  CT3 9   180.0012.552000 2 ; 
inserted for HIC
  HR2 CPH2  NR3  CT3 9   180.0012.552000 2 ; 
inserted for HIC
  HR1 CPH1  NR3  CT3 9 0.0008.368000 2 ; 
inserted for HIC
 CPH1 CPH1  NR3  CT3 9   180.0050.208000 2 ; 
inserted for HIC
  CT1  CT2 CPH1  NR3 9 0.0  0.00 1 ; 
inserted for HIC
 CPH1  NR3  CT3  HA3 9 0.0  0.00 1 ; 
inserted for HIC
 CPH2  NR3  CT3  HA3 9 0.00 0.00 1 ; 
inserted for HIC
[ dihedraltypes ]
; 'improper' dihedrals
;  ijkl  func phi0 kphi
  NR3 CPH1 CPH2  CT3 2 0.  10.041600 ; inserted 
for HIC
  NR3 CPH2 CPH1  CT3 2 0.0 10.041600 ; inserted 
for HIC
  CT2 CPH1  NR3 CPH1 2 0.0  0.0  ; inserted 
for HIC
  CT2  NR3 CPH1 CPH1 2 0.0  0.0  ; inserted 
for HIC
 CPH1 CPH1  NR3  HR1 2 0.0  0.0 ; inserted 
for HIC
 CPH1  NR3 CPH1  HR1 2 0.0  0.0 ; inserted 
for HIC
 CPH2  NR3  NR3  HR2 2 0.0  0.0 ; inserted 
for HIC

but ended up with "No default U-B types" for CPH1 NR3 CT3 and CPH2 NR3 CT3
Anyone who is interested to help me find the problem?

Or is there a better atomtype for the nitrogen in the HIS/imidazole ring where 
a methyl group can be attached. I tried NG321, but then I ran into troubles 
when attaching to CPH1 and CPH2.



Don't mix CGenFF types with normal CHARMM types.

All you need to do is find an analogous angle to CPH1(2)-NR3-CT3.  There are 
methylated nucleobases in CHARMM that you can look at, which the thread you 
quote mentions.


-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] Automake problem during installation 4.5.7

[Justin Lemkul]

On 7/4/17 11:56 PM, CHEN, Yu Wai [ABCT] wrote:

Dear all,

I am trying to install 4.5.7 (because I need to use a forcefield which is for 4.5.X) with MPI on our system 


Any force field that is in the format of version 4.5 is compatible with all 
newer GROMACS versions.  I recommend that you don't try to install antiquated 
and unsupported software.  Old code on newer hardware, with newer compilers 
rarely works.  Try the latest version of GROMACS.


-Justin

here which runs Scientific Linux 6.3. I managed to do some SETENV to get the 
library and include paths set up, and

configure finished without issues. But when I tried to do "make", it gives me 
errors:

./configure: line 2050: syntax error near unexpected token `tar-ustar'
./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)'
make: *** [config.status] Error 2

I searched on the internet, someone asked the same question in 2013; an answer 
suggested to comment out the AM_INIT_AUTOMAKE(tar-ustar) line in configure.ac 
which I tried but did not work; i.e. led to other automake problems.

Can someone help me? Thanks.


--
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Hong Kong Polytechnic University   +852-34008660
Department of Applied Biology & Chemical Technology


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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] Number of ions in Anionic lipid system- Charmm-GUI

[Justin Lemkul]

On 7/4/17 9:20 PM, Nidhin Thomas wrote:

Dear GROMACS Users,

I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI.
I want to include 0.150 M KCl in the system. When I use the option in 
charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number 
of ions using the size of simulation box, I am getting 98 ions.

Can anyone tell me what I should do to get the exact number of ions in the 
system?



CHARMM-GUI calculates an excluded volume due to the solute (protein, nucleic 
acid, lipids, etc) so using the total box volume is incorrect when calculating 
the number of ions in solution.  The result you're getting tells you that your 
box is too small (insufficient solvent volume) to achieve 150 mM KCl.



Would it be correct if I first neutralize the system using 100 K+ ions and then 
add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system?



No, because then your effective concentration is much higher than what you want.

-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] Ligand and ion topology

[Justin Lemkul]

On 7/4/17 5:33 AM, Khadija Amine wrote:

Dear gromacs users,

I have a protein with GNP ligand and acetate ACT ion that I want to
simulate.

I have prepared topologies for both GNP and ACT with PRODRG program.



Don't use PRODRG unless you manually reparametrize the charges and charge groups 
afterward.



My first question is: Where should I exactly include the ACT.itp and
GNP.itp into topol.top file?



In principle, anywhere after the initial force field #include statement, as long 
as no new parameter types are introduced.



My second question is:
I have Copied and pasted the coordinates from my two molecules files onto
the end of the protein.gro file. I have changed the number at the top or
beginning of the file from as it should be to corrected the total number of
atoms in the file.

Should I change the atom number column and renumber the atoms with the new
ones?



mdrun doesn't care about coordinate file numbering.


Is this will affect the position of the ligand and the ions in the protein
structure?



Only coordinates affect positions, not atom numbers.

-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' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs

[Justin Lemkul]

On 7/4/17 12:31 AM, SOMNATH JAN wrote:

Dear Users,
I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for
a RNA that has phosphate (P, OP1, OP2, OP3) on 5' .
As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5'
of RNA, pdb2gmx is giving an error.
And so I want to add a 5'terminal PHOSPHATE patch (5PHO) in charmm36
forcefield. Parameters for 5PHO are available in CHARMM force field files
in internet (top_all36_na.rtf - PRES 5PHO), but the charge units of atoms
and the way of entry is completely different for CHARMM and Gromacs. So how
will I make a new entry of 5PHO in Charmm36 by taking the parameters from
CHARMM force field files?

Another thing, there is no 'rna.n.tdb' file available for Charmm36 force
field, so where will I make the new entry of 5PHO?



You'll put it in merged.n.tdb - our port doesn't make a distinction between 
termini types (amino acids, DNA, RNA, etc).  It's a limitation of how we 
generate the files.


The information is almost identical to what one finds in the GROMACS files - 
atom names, types, and charges.  You'll just have two blocks, [add] and [replace].


-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] protein protein interaction: side chain contribution

[Justin Lemkul]

On 7/3/17 4:20 AM, Tushar Ranjan Moharana wrote:

Hi all,
I want to know the contribution of various amino acid side chain in complex
that composed of 2 proteins. I used GROMOS53a6 forcefiel for the
simulation. All parameters are as recommended by the concerned paper. I
made separate index groups for each amino acid side chain and the proteins.
I calculated Coulomb and LJ interaction using gmx energ between the amino
acid and the interacting protein. Following are few results, I obtained:

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Coul-SR:161TYR-Protein_B   -74.03971.917.83648.11782
(kJ/mol)
LJ-SR:161TYR-Protein_B -49.5351.510.29262.73416
(kJ/mol)
Coul-14:161TYR-Protein_B  0  0  0  0
(kJ/mol)
LJ-14:161TYR-Protein_B-1.20657  0.088   0.533195   0.474622
(kJ/mol)

where Protein_B is the other protein in the complex. I have following
doubts.
1) Energy I obtained looks too high to me. Is everything correct? I
searched for information but couldn't get much, so don't know what should
be the ideal values. Results might be correct but I am not sure.



I don't know how you're making this assessment.  Your numbers look to be of 
reasonable magnitude, though I'm not sure how you have a 1-4 term between 
different protein units.  Check your index groups.



2) How can I calculate kinetic energy of the amino acid side chain? gmx
traj or energy(after saving only desired atoms in the trajectory) which one
will be more meaning full?



You can do it either way, but I would argue that neither is actually meaningful.

-Justin


Kindly help me at least in the first question. Any kind of
informations/suggestions are most welcom.

Thanks for your valuable time and efforts.


"A society with free knowledge is better than a society with free food"



--
==

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] Flat-bottom spherical potential

[Shraddha Parate]

Hello all,

I had emailed to Gromacs Users List the following query as per the attached
thread (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
users/2017-June/114166.html)

Justin mentioned about applying a flat-bottom spherical potential which
will keep the droplet formed on the surface. I tried my best to figure out
the corresponding file to implement the potential, but could not find. Can
anyone please let me know more clearly on how I can make this kind of
changes?

Thank you in advance,
Regards
Shraddha
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[gmx-users] Gromacs 5.0 - Solvent Accessible Surface Area (sasa) separate Hydrophobic and Hydrophilic components

[Nuria Codina]

Hi,

I would like to measure the Hydrophobic and Hydrophilic components of
the Solvent Accessible Surface Area. In the Tool Changes for 5.0 I found
these command:

gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output
'"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B"
and not charge {-0.2 to 0.2}; "Total" group "B"'

But I get this error:

Error: Multiple groups 'A' selected

Inconsistency in user input:
Invalid index group reference(s)
  Cannot match 'group "A"', because no such index group can be found.

Can you let me know how to define the selection?
I've tried "group 1" and "group protein" as well, but it doesn't recognize
it either.

Many thanks in advance,
Núria
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[gmx-users] Acetonitrile and isopropanol with CHARMM ff

[Sonia Milena Aguilera Segura]

Dear GROMACS users, 

I am currently interested in studying properties of some solvents, among them 
acetonitrile and isopropanol. I would like to use CHARMM force field for 
compatibility with other molecules and I am taking my initial structure files 
from virtualchemistry.org. Does someone know how to run the 6-sites model 
available with the CHARMM ff in gromacs? As I try to run the simulation box I 
get the error "No Defaul Proper Dih. Types". I checked the ffbonded file and I 
didn't see the dihedrals defined as in the rtp file. And for what I've 
understood this is because acetonitrile is a linear molecule and dihedrals for 
three colinear atoms this are mathematically undefined. Also, when I go to 
check the available itp for acetonitrile in virtualchemistry.org, I can see 
that there is a 7-sites model,with a dummy atom included. However, for this 
case, pdb and itp files do not match. I have seen that this can be sort of 
solved by fixing the angle as 179.9, but I really don't exactly what to change
  or where in the force field files. I have no experience modifying force 
fields. Also, I've seen that for the opls ff both pdb and itp files match, but 
I really need to use the CHARMM force field. Are the opls parameters compatible 
with CHARMM? Any advice? 

Also, I cannot find an already optimized structure with all hydrogens for 
isopropanol. Could somenone provide one? 

Thank you very much in advance for your time and help!! 

Best regards, 

Sonia Aguilera 
PhD student 
ENSCM 
Montpellier, France 

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