Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Great!

I had already setup my git copy. No need for it. Strange atom names as
usual.

So we can already start our metalloenzyme simulation.

Great software and support.
Thank you Mark and Justin!

2016-04-22 21:49 GMT-03:00 Justin Lemkul :

>
>
> On 4/22/16 8:40 PM, Pedro Lacerda wrote:
>
>> Applying the same simple conversion to the vdw parameters for atoms Mg+2
>> (id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER
>> package, which is the base of Sorin parameters, there is agreement between
>> Mg+2 and Zn+2.
>>
>> It looks like a bug in the L-J parameters of TINKER package for amber99*
>> force fields. If it becomes confirmed, should I fill an issue at Redmine
>> or
>> request a code review?
>>
>> However I may be wrong...
>>
>> http://dasher.wustl.edu/tinker/distribution/params/amber99.prm
>>
>>
> You're not looking at the right parameters.  What you've claimed to be
> Ca2+ from ffnonbonded.itp is:
>
> Ca2+ 3.40E-01 3.60E-01
>
> But it's not.  The calcium atom type is C0 (see ions.itp):
>
> C0  20  40.080.  A   3.05240e-01  1.92376e+00
>
> If you run your conversion on the right parameters you will see it matches
> exactly.
>
> -Justin
>
>
> 2016-04-22 20:11 GMT-03:00 Pedro Lacerda :
>>
>> For me they must be the same in both force fields amber99sb-ildn, amber99,
>>> at the paper, etc. If it is different then should be another force field,
>>> isn't it?
>>>
>>> About the conversion, I did it wrong on my spreadsheet. Sorry...
>>>
>>> It works! Many thanks!
>>>
>>> Except for the epsilon of Ca+2. I verified the parameters of atom
>>> amber99_15  (Ca +2) in ffamber_v4.0/ffamber99sb/ffamber99sbsbnb.itp and,
>>> of
>>> course, is the same of GROMACS files, but it is different than the
>>> previously referred paper.
>>>
>>> I also checked the parameters in amber10.ffparms.tar.bz2/parm/parm99.dat,
>>> and it agreed with paper, disagreeing with GROMACS.
>>>
>>> Just a small question, PARM is the file format for force fields in AMBER,
>>> right?
>>>
>>> http://ffamber.cnsm.csulb.edu/ffamber.php
>>> http://ambermd.org/dbase.html
>>>
>>>
>>>
>>> 2016-04-22 19:29 GMT-03:00 Justin Lemkul :
>>>
>>>

 On 4/22/16 6:24 PM, Pedro Lacerda wrote:

 Thank you!
>
> According to [1, Table 2a], these are the L-J (6-12) parameters for
> Ca2+
> used at AMBER package. Or the paper or GROMACS copied wrongly from the
> AMBER package source because simple unit conversion gives different
> results.
>
>
> That paper was published 3 years after AMBER99SB-ILDN so expecting
 those
 parameters to be in that force field implementation is wrong.  There
 could
 be a mistake but the AMBER ports have been extensively verified.  There
 are
 lots of AMBER-compatible ion parameters floating around, though.

 I don't own a copy of AMBER package, please could you verify the Ca L-J

> parameters for me?
>
>
> The AMBER force fields should be freely available (I don't use AMBER
 software).

 And I can't see how your conversion formula from Rmin/2 to sigma could

> produce the right result.
>
>
> Plug in the values, it works.  It's the same conversion for CHARMM.
 For
 instance, Mg2+:

 1.1 * 2 * 2^(-1/6) * 0.1 = 0.196

 -Justin


 [1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.

> doi:10.1021/ct400146w.
>
> 2016-04-21 23:35 GMT-03:00 Justin Lemkul :
>
>
>
>> On 4/21/16 4:30 PM, Pedro Lacerda wrote:
>>
>> Hi Mark,
>>
>>>
>>> I starting converting from AMBER (according to the paper) to GROMACS
>>> and
>>> comparing the results.
>>>
>>> Please explain in more words what this constant of two mean or how
>>> can
>>> I
>>> handle it. Ignoring it and just converting the units, I got these
>>> results
>>>
>>>
>>> It's force field convention, just different notation.  Sometimes
>>>
>> different
>> force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
>> converted, e.g.:
>>
>> sigma = (Rmin/2)*2*2^(-1/6)
>>
>> and in GROMACS the units are nm so you need an additional
>> multiplication
>> by 0.1 to convert A -> nm.
>>
>> AMBER (table 2a)
>>
>> Rmin/2 (Å) epsilon (kcal/mol)
>>> Zn2+ 1.10E+00 1.25E-02
>>> Mg2+ 7.93E-01 8.95E-01
>>> Ca2+ 1.71E+00 4.60E-01
>>> AMBER converted
>>> R (nm) epsilon (kJ/mol)
>>> Zn2+ 2.20E+01 5.23E-02
>>> Mg2+ 1.59E+01 3.74E+00
>>> Ca2+ 3.43E+01 1.92E+00
>>>
>>> amber99sb-ildn.ff/ffnonbonded.itp
>>> sigma (nm) epsilon (kJ/mol)
>>> Zn2+ 1.96E-01 5.23E-02
>>> Mg2+ 1.41E-01 3.74E+00
>>> Ca2+ 3.40E-01 3.60E-01
>>>
>>> I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also
>>> the
>>> difference 

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Justin Lemkul]

On 4/22/16 8:40 PM, Pedro Lacerda wrote:

Applying the same simple conversion to the vdw parameters for atoms Mg+2
(id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER
package, which is the base of Sorin parameters, there is agreement between
Mg+2 and Zn+2.

It looks like a bug in the L-J parameters of TINKER package for amber99*
force fields. If it becomes confirmed, should I fill an issue at Redmine or
request a code review?

However I may be wrong...

http://dasher.wustl.edu/tinker/distribution/params/amber99.prm



You're not looking at the right parameters.  What you've claimed to be Ca2+ from 
ffnonbonded.itp is:


Ca2+ 3.40E-01 3.60E-01

But it's not.  The calcium atom type is C0 (see ions.itp):

C0  20  40.080.  A   3.05240e-01  1.92376e+00

If you run your conversion on the right parameters you will see it matches 
exactly.

-Justin


2016-04-22 20:11 GMT-03:00 Pedro Lacerda :


For me they must be the same in both force fields amber99sb-ildn, amber99,
at the paper, etc. If it is different then should be another force field,
isn't it?

About the conversion, I did it wrong on my spreadsheet. Sorry...

It works! Many thanks!

Except for the epsilon of Ca+2. I verified the parameters of atom
amber99_15  (Ca +2) in ffamber_v4.0/ffamber99sb/ffamber99sbsbnb.itp and, of
course, is the same of GROMACS files, but it is different than the
previously referred paper.

I also checked the parameters in amber10.ffparms.tar.bz2/parm/parm99.dat,
and it agreed with paper, disagreeing with GROMACS.

Just a small question, PARM is the file format for force fields in AMBER,
right?

http://ffamber.cnsm.csulb.edu/ffamber.php
http://ambermd.org/dbase.html



2016-04-22 19:29 GMT-03:00 Justin Lemkul :




On 4/22/16 6:24 PM, Pedro Lacerda wrote:


Thank you!

According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
used at AMBER package. Or the paper or GROMACS copied wrongly from the
AMBER package source because simple unit conversion gives different
results.



That paper was published 3 years after AMBER99SB-ILDN so expecting those
parameters to be in that force field implementation is wrong.  There could
be a mistake but the AMBER ports have been extensively verified.  There are
lots of AMBER-compatible ion parameters floating around, though.

I don't own a copy of AMBER package, please could you verify the Ca L-J

parameters for me?



The AMBER force fields should be freely available (I don't use AMBER
software).

And I can't see how your conversion formula from Rmin/2 to sigma could

produce the right result.



Plug in the values, it works.  It's the same conversion for CHARMM.  For
instance, Mg2+:

1.1 * 2 * 2^(-1/6) * 0.1 = 0.196

-Justin


[1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.

doi:10.1021/ct400146w.

2016-04-21 23:35 GMT-03:00 Justin Lemkul :




On 4/21/16 4:30 PM, Pedro Lacerda wrote:

Hi Mark,


I starting converting from AMBER (according to the paper) to GROMACS
and
comparing the results.

Please explain in more words what this constant of two mean or how can
I
handle it. Ignoring it and just converting the units, I got these
results


It's force field convention, just different notation.  Sometimes

different
force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
converted, e.g.:

sigma = (Rmin/2)*2*2^(-1/6)

and in GROMACS the units are nm so you need an additional multiplication
by 0.1 to convert A -> nm.

AMBER (table 2a)


Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.


See above for the proper way to convert Rmin/2 to sigma.


As for Ca, probably the parameters are coming from a different source.
I
don't know what "Table 2a" means or what paper it's from, but you need
to
verify that the source of parameters is compatible or that you
understand
where differences are coming from.

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read 

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Applying the same simple conversion to the vdw parameters for atoms Mg+2
(id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER
package, which is the base of Sorin parameters, there is agreement between
Mg+2 and Zn+2.

It looks like a bug in the L-J parameters of TINKER package for amber99*
force fields. If it becomes confirmed, should I fill an issue at Redmine or
request a code review?

However I may be wrong...

http://dasher.wustl.edu/tinker/distribution/params/amber99.prm

2016-04-22 20:11 GMT-03:00 Pedro Lacerda :

> For me they must be the same in both force fields amber99sb-ildn, amber99,
> at the paper, etc. If it is different then should be another force field,
> isn't it?
>
> About the conversion, I did it wrong on my spreadsheet. Sorry...
>
> It works! Many thanks!
>
> Except for the epsilon of Ca+2. I verified the parameters of atom
> amber99_15  (Ca +2) in ffamber_v4.0/ffamber99sb/ffamber99sbsbnb.itp and, of
> course, is the same of GROMACS files, but it is different than the
> previously referred paper.
>
> I also checked the parameters in amber10.ffparms.tar.bz2/parm/parm99.dat,
> and it agreed with paper, disagreeing with GROMACS.
>
> Just a small question, PARM is the file format for force fields in AMBER,
> right?
>
> http://ffamber.cnsm.csulb.edu/ffamber.php
> http://ambermd.org/dbase.html
>
>
>
> 2016-04-22 19:29 GMT-03:00 Justin Lemkul :
>
>>
>>
>> On 4/22/16 6:24 PM, Pedro Lacerda wrote:
>>
>>> Thank you!
>>>
>>> According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
>>> used at AMBER package. Or the paper or GROMACS copied wrongly from the
>>> AMBER package source because simple unit conversion gives different
>>> results.
>>>
>>>
>> That paper was published 3 years after AMBER99SB-ILDN so expecting those
>> parameters to be in that force field implementation is wrong.  There could
>> be a mistake but the AMBER ports have been extensively verified.  There are
>> lots of AMBER-compatible ion parameters floating around, though.
>>
>> I don't own a copy of AMBER package, please could you verify the Ca L-J
>>> parameters for me?
>>>
>>>
>> The AMBER force fields should be freely available (I don't use AMBER
>> software).
>>
>> And I can't see how your conversion formula from Rmin/2 to sigma could
>>> produce the right result.
>>>
>>>
>> Plug in the values, it works.  It's the same conversion for CHARMM.  For
>> instance, Mg2+:
>>
>> 1.1 * 2 * 2^(-1/6) * 0.1 = 0.196
>>
>> -Justin
>>
>>
>> [1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.
>>> doi:10.1021/ct400146w.
>>>
>>> 2016-04-21 23:35 GMT-03:00 Justin Lemkul :
>>>
>>>

 On 4/21/16 4:30 PM, Pedro Lacerda wrote:

 Hi Mark,
>
> I starting converting from AMBER (according to the paper) to GROMACS
> and
> comparing the results.
>
> Please explain in more words what this constant of two mean or how can
> I
> handle it. Ignoring it and just converting the units, I got these
> results
>
>
> It's force field convention, just different notation.  Sometimes
 different
 force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
 converted, e.g.:

 sigma = (Rmin/2)*2*2^(-1/6)

 and in GROMACS the units are nm so you need an additional multiplication
 by 0.1 to convert A -> nm.

 AMBER (table 2a)

> Rmin/2 (Å) epsilon (kcal/mol)
> Zn2+ 1.10E+00 1.25E-02
> Mg2+ 7.93E-01 8.95E-01
> Ca2+ 1.71E+00 4.60E-01
> AMBER converted
> R (nm) epsilon (kJ/mol)
> Zn2+ 2.20E+01 5.23E-02
> Mg2+ 1.59E+01 3.74E+00
> Ca2+ 3.43E+01 1.92E+00
>
> amber99sb-ildn.ff/ffnonbonded.itp
> sigma (nm) epsilon (kJ/mol)
> Zn2+ 1.96E-01 5.23E-02
> Mg2+ 1.41E-01 3.74E+00
> Ca2+ 3.40E-01 3.60E-01
>
> I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
> difference on sigma was in the order Å/10, except for Zn which was
> relatively significant.
>
>
> See above for the proper way to convert Rmin/2 to sigma.

 As for Ca, probably the parameters are coming from a different source.
 I
 don't know what "Table 2a" means or what paper it's from, but you need
 to
 verify that the source of parameters is compatible or that you
 understand
 where differences are coming from.

 -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 

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

For me they must be the same in both force fields amber99sb-ildn, amber99,
at the paper, etc. If it is different then should be another force field,
isn't it?

About the conversion, I did it wrong on my spreadsheet. Sorry...

It works! Many thanks!

Except for the epsilon of Ca+2. I verified the parameters of atom
amber99_15  (Ca +2) in ffamber_v4.0/ffamber99sb/ffamber99sbsbnb.itp and, of
course, is the same of GROMACS files, but it is different than the
previously referred paper.

I also checked the parameters in amber10.ffparms.tar.bz2/parm/parm99.dat,
and it agreed with paper, disagreeing with GROMACS.

Just a small question, PARM is the file format for force fields in AMBER,
right?

http://ffamber.cnsm.csulb.edu/ffamber.php
http://ambermd.org/dbase.html



2016-04-22 19:29 GMT-03:00 Justin Lemkul :

>
>
> On 4/22/16 6:24 PM, Pedro Lacerda wrote:
>
>> Thank you!
>>
>> According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
>> used at AMBER package. Or the paper or GROMACS copied wrongly from the
>> AMBER package source because simple unit conversion gives different
>> results.
>>
>>
> That paper was published 3 years after AMBER99SB-ILDN so expecting those
> parameters to be in that force field implementation is wrong.  There could
> be a mistake but the AMBER ports have been extensively verified.  There are
> lots of AMBER-compatible ion parameters floating around, though.
>
> I don't own a copy of AMBER package, please could you verify the Ca L-J
>> parameters for me?
>>
>>
> The AMBER force fields should be freely available (I don't use AMBER
> software).
>
> And I can't see how your conversion formula from Rmin/2 to sigma could
>> produce the right result.
>>
>>
> Plug in the values, it works.  It's the same conversion for CHARMM.  For
> instance, Mg2+:
>
> 1.1 * 2 * 2^(-1/6) * 0.1 = 0.196
>
> -Justin
>
>
> [1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.
>> doi:10.1021/ct400146w.
>>
>> 2016-04-21 23:35 GMT-03:00 Justin Lemkul :
>>
>>
>>>
>>> On 4/21/16 4:30 PM, Pedro Lacerda wrote:
>>>
>>> Hi Mark,

 I starting converting from AMBER (according to the paper) to GROMACS and
 comparing the results.

 Please explain in more words what this constant of two mean or how can I
 handle it. Ignoring it and just converting the units, I got these
 results


 It's force field convention, just different notation.  Sometimes
>>> different
>>> force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
>>> converted, e.g.:
>>>
>>> sigma = (Rmin/2)*2*2^(-1/6)
>>>
>>> and in GROMACS the units are nm so you need an additional multiplication
>>> by 0.1 to convert A -> nm.
>>>
>>> AMBER (table 2a)
>>>
 Rmin/2 (Å) epsilon (kcal/mol)
 Zn2+ 1.10E+00 1.25E-02
 Mg2+ 7.93E-01 8.95E-01
 Ca2+ 1.71E+00 4.60E-01
 AMBER converted
 R (nm) epsilon (kJ/mol)
 Zn2+ 2.20E+01 5.23E-02
 Mg2+ 1.59E+01 3.74E+00
 Ca2+ 3.43E+01 1.92E+00

 amber99sb-ildn.ff/ffnonbonded.itp
 sigma (nm) epsilon (kJ/mol)
 Zn2+ 1.96E-01 5.23E-02
 Mg2+ 1.41E-01 3.74E+00
 Ca2+ 3.40E-01 3.60E-01

 I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
 difference on sigma was in the order Å/10, except for Zn which was
 relatively significant.


 See above for the proper way to convert Rmin/2 to sigma.
>>>
>>> As for Ca, probably the parameters are coming from a different source.  I
>>> don't know what "Table 2a" means or what paper it's from, but you need to
>>> verify that the source of parameters is compatible or that you understand
>>> where differences are coming from.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> 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
> 

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Justin Lemkul]

On 4/22/16 6:24 PM, Pedro Lacerda wrote:

Thank you!

According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
used at AMBER package. Or the paper or GROMACS copied wrongly from the
AMBER package source because simple unit conversion gives different results.



That paper was published 3 years after AMBER99SB-ILDN so expecting those 
parameters to be in that force field implementation is wrong.  There could be a 
mistake but the AMBER ports have been extensively verified.  There are lots of 
AMBER-compatible ion parameters floating around, though.



I don't own a copy of AMBER package, please could you verify the Ca L-J
parameters for me?



The AMBER force fields should be freely available (I don't use AMBER software).


And I can't see how your conversion formula from Rmin/2 to sigma could
produce the right result.



Plug in the values, it works.  It's the same conversion for CHARMM.  For 
instance, Mg2+:


1.1 * 2 * 2^(-1/6) * 0.1 = 0.196

-Justin


[1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.
doi:10.1021/ct400146w.

2016-04-21 23:35 GMT-03:00 Justin Lemkul :




On 4/21/16 4:30 PM, Pedro Lacerda wrote:


Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results



It's force field convention, just different notation.  Sometimes different
force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
converted, e.g.:

sigma = (Rmin/2)*2*2^(-1/6)

and in GROMACS the units are nm so you need an additional multiplication
by 0.1 to convert A -> nm.

AMBER (table 2a)

Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.



See above for the proper way to convert Rmin/2 to sigma.

As for Ca, probably the parameters are coming from a different source.  I
don't know what "Table 2a" means or what paper it's from, but you need to
verify that the source of parameters is compatible or that you understand
where differences are coming from.

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

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] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Thank you!

According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
used at AMBER package. Or the paper or GROMACS copied wrongly from the
AMBER package source because simple unit conversion gives different results.

I don't own a copy of AMBER package, please could you verify the Ca L-J
parameters for me?

And I can't see how your conversion formula from Rmin/2 to sigma could
produce the right result.

[1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.
doi:10.1021/ct400146w.

2016-04-21 23:35 GMT-03:00 Justin Lemkul :

>
>
> On 4/21/16 4:30 PM, Pedro Lacerda wrote:
>
>> Hi Mark,
>>
>> I starting converting from AMBER (according to the paper) to GROMACS and
>> comparing the results.
>>
>> Please explain in more words what this constant of two mean or how can I
>> handle it. Ignoring it and just converting the units, I got these results
>>
>>
> It's force field convention, just different notation.  Sometimes different
> force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
> converted, e.g.:
>
> sigma = (Rmin/2)*2*2^(-1/6)
>
> and in GROMACS the units are nm so you need an additional multiplication
> by 0.1 to convert A -> nm.
>
> AMBER (table 2a)
>> Rmin/2 (Å) epsilon (kcal/mol)
>> Zn2+ 1.10E+00 1.25E-02
>> Mg2+ 7.93E-01 8.95E-01
>> Ca2+ 1.71E+00 4.60E-01
>> AMBER converted
>> R (nm) epsilon (kJ/mol)
>> Zn2+ 2.20E+01 5.23E-02
>> Mg2+ 1.59E+01 3.74E+00
>> Ca2+ 3.43E+01 1.92E+00
>>
>> amber99sb-ildn.ff/ffnonbonded.itp
>> sigma (nm) epsilon (kJ/mol)
>> Zn2+ 1.96E-01 5.23E-02
>> Mg2+ 1.41E-01 3.74E+00
>> Ca2+ 3.40E-01 3.60E-01
>>
>> I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
>> difference on sigma was in the order Å/10, except for Zn which was
>> relatively significant.
>>
>>
> See above for the proper way to convert Rmin/2 to sigma.
>
> As for Ca, probably the parameters are coming from a different source.  I
> don't know what "Table 2a" means or what paper it's from, but you need to
> verify that the source of parameters is compatible or that you understand
> where differences are coming from.
>
> -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] Adapting metallic ions from AMBER to GROMACS

[Justin Lemkul]

On 4/21/16 4:30 PM, Pedro Lacerda wrote:

Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results



It's force field convention, just different notation.  Sometimes different force 
fields or programs use Rmin/2, Rmin, or sigma.  They're easily converted, e.g.:


sigma = (Rmin/2)*2*2^(-1/6)

and in GROMACS the units are nm so you need an additional multiplication by 0.1 
to convert A -> nm.



AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.



See above for the proper way to convert Rmin/2 to sigma.

As for Ca, probably the parameters are coming from a different source.  I don't 
know what "Table 2a" means or what paper it's from, but you need to verify that 
the source of parameters is compatible or that you understand where differences 
are coming from.


-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] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results

AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.

(I'm expecting that Mailman render the table into plain text relatively
well, so if this post go with bad formatting I'll post again)

Very thanks
Pedro


2016-04-18 21:29 GMT-03:00 Mark Abraham :

> Hi,
>
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
>
> Mark
>
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:
>
> > Hi Gromacs users,
> >
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in [1] cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> > slightly different.
> >
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> based
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> in
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> >
> > Eq 1:
> >
> > Lj = 4e ((R/r)^12 - (R/r)^6)
> >
> > Eq 4.5:
> >
> > Lj = e ((R/r)^12 - 2(R/r)^6)
> >
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> >
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> >
> > (Sorry about the previous email, now the title is correct)
> >
> > [1]
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >
> > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >
> > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> >
> >
> > Cheers,
> >
> > Pedro Lacerda
> > --
> > 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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> >
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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Very thanks,

I'm trying it right now.

Pedro Lacerda

2016-04-18 21:29 GMT-03:00 Mark Abraham :

> Hi,
>
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
>
> Mark
>
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:
>
> > Hi Gromacs users,
> >
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in [1] cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> > slightly different.
> >
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> based
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> in
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> >
> > Eq 1:
> >
> > Lj = 4e ((R/r)^12 - (R/r)^6)
> >
> > Eq 4.5:
> >
> > Lj = e ((R/r)^12 - 2(R/r)^6)
> >
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> >
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> >
> > (Sorry about the previous email, now the title is correct)
> >
> > [1]
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >
> > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >
> > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> >
> >
> > Cheers,
> >
> > Pedro Lacerda
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Mark Abraham]

Hi,

Convert the units and absorb the factor of two to the minus six. Compare
with other ions present in both representations of such force fields.

Mark

On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:

> Hi Gromacs users,
>
> We are planning a simulation with a metallic (fe+2) attached on the
> protein. The parameters found in [1] cannot be directly inserted on
> ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> slightly different.
>
> Theoreticaly these Lennard-Jones parameters could be used in any PME based
> force field, but it was derived and tested using the AMBER software and
> potential, so it is our current force field of choice. In
> amber99sb-ildn/ffnonbonded.itp the long range interactions are described in
> terms of epsilon (kJ/mol) and sigma (Rmin; nm).
>
> Eq 1:
>
> Lj = 4e ((R/r)^12 - (R/r)^6)
>
> Eq 4.5:
>
> Lj = e ((R/r)^12 - 2(R/r)^6)
>
> Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> calculations to optimize the software. But this occurs at implementation
> level and probably does not have correspondence with the paper.
>
> My question is how can I adapt these parameters so they can be used in
> Gromacs?
>
> (Sorry about the previous email, now the title is correct)
>
> [1]
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
>
> [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
>
> [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
>
>
> Cheers,
>
> Pedro Lacerda
> --
> Gromacs Users mailing list
>
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> posting!
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