Re: [gmx-users] genion question

2009-08-25 Thread Justin A. Lemkul



Paymon Pirzadeh wrote:

Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:



You chose the wrong terminus.  The Zwitterion-NH3+ species is for an isolated 
amino acid containing both NH3+ and COO- alpha-carbon substituents.  Choose a 
plain NH3+ for your terminus.


-Justin


 1   opls_287  1ASP  N  1   -0.314.0067   ; qtot
-0.3
 2   opls_290  1ASP H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1ASP H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1ASP H3  1   0.33  1.008   ;
qtot 0.69
 5   opls_299  1ASP CA  1   0.15 12.011   ;
qtot 0.84
 6   opls_140  1ASP HA  1   0.06  1.008   ;
qtot 0.9
 7   opls_274  1ASP CB  2  -0.22 12.011   ;
qtot 0.68
 8   opls_140  1ASPHB1  2   0.06  1.008   ;
qtot 0.74
 9   opls_140  1ASPHB2  2   0.06  1.008   ;
qtot 0.8
10   opls_271  1ASP CG  30.7 12.011   ;
qtot 1.5
11   opls_272  1ASPOD1  3   -0.815.9994   ;
qtot 0.7
12   opls_272  1ASPOD2  3   -0.815.9994   ;
qtot -0.1
13   opls_235  1ASP  C  40.5 12.011   ;
qtot 0.4
14   opls_236  1ASP  O  4   -0.515.9994   ;
qtot -0.1

What do you think?

Payman





On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!

The total charge will undoubtedly fluctuate.  What's most important to look at 
is when you reach the end of a residue and you do not see an integer charge.


-Justin


Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the

No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post

Re: [gmx-users] genion question

2009-08-25 Thread Paymon Pirzadeh
Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:

 1   opls_287  1ASP  N  1   -0.314.0067   ; qtot
-0.3
 2   opls_290  1ASP H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1ASP H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1ASP H3  1   0.33  1.008   ;
qtot 0.69
 5   opls_299  1ASP CA  1   0.15 12.011   ;
qtot 0.84
 6   opls_140  1ASP HA  1   0.06  1.008   ;
qtot 0.9
 7   opls_274  1ASP CB  2  -0.22 12.011   ;
qtot 0.68
 8   opls_140  1ASPHB1  2   0.06  1.008   ;
qtot 0.74
 9   opls_140  1ASPHB2  2   0.06  1.008   ;
qtot 0.8
10   opls_271  1ASP CG  30.7 12.011   ;
qtot 1.5
11   opls_272  1ASPOD1  3   -0.815.9994   ;
qtot 0.7
12   opls_272  1ASPOD2  3   -0.815.9994   ;
qtot -0.1
13   opls_235  1ASP  C  40.5 12.011   ;
qtot 0.4
14   opls_236  1ASP  O  4   -0.515.9994   ;
qtot -0.1

What do you think?

Payman





On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Well, when I look into my .top file, almost no where I see closeness to
> > an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
> > sometimes. But I can not see a clear trend on where things go wrong. My
> > protein has only 37 amino acids with 451 atoms (including hydrogens).
> > I am not sure if I can attach the .top file to my e-mail for you to
> > check. This way I could learn where and how things go wrong!
> > 
> 
> The total charge will undoubtedly fluctuate.  What's most important to look 
> at 
> is when you reach the end of a residue and you do not see an integer charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Thanks for the tips!
> >>> But I still have problem with my added ion. Justin had told me that ion
> >>> names are force-field specific! Since I am using OPLSaa, I checked the
> >>> itp file for Na ion name, and it was Na+. I used this name with the
> >> No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:
> >>
> >> [ moleculetype ]
> >> ; molname   nrexcl
> >> NA+ 1
> >>
> >> [ atoms ]
> >> ; idat type res nr  residu name at name  cg nr  charge   
> >> mass
> >> 1   opls_4071   NA+ NA   1  1   
> >> 22.98977
> >>
> >>> -pname switch, but again during the grompp I ran into the following
> >>> error:
> >>> Warning: atom name 65870 in AFP_I.top and
> >>> AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> >>>
> >>> WARNING 1 [file AFP_I.top, line 4151]:
> >>>   1 non-matching atom name
> >>>   atom names from AFP_I.top will be used
> >>>   atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> >>>
> >>> I really do not know what I am doing wrong here! Also regarding past
> >>> discussions, adding this single ion has lead into the following note:
> >>>  
> >>> NOTE 1 [file AFP_I.top, line 4151]:
> >>>   System has non-zero total charge: 1.00e-02
> >>>
> >>> I am not sure if that much charge will cause me troubles or not!
> >>>
> >> I am somewhat troubled by the magnitude of charge discrepancy.  Look in 
> >> the .top 
> >> to see where things start going wrong (i.e., not an integer).  I would 
> >> think 
> >> your system would have to be quite large to accumulate such a difference 
> >> in charge.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
>  Paymon Pirzadeh wrote:
> > Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> > negative charge exactly? Does that hurt science or simulation?
>  It's probably irrelevant. The representation of "decimal" numbers on 
>  computers can be inexact, such that things like 0.02 added to itself 100 
>  times does not pass a test for equality with 2. You may be observing 
>  this kind of thing here. Your protein's [atoms] directive has a running 
>  count of the total  charge on the molecule - go and read it and see that 
>  each residue has an integral charge. Hopefully you can observe where the 
>  rounding error might be occurring and you can make a judgement about 
>  whether this might be true.
> 
>  Mark
>  ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://lists.gromacs.org/m

Re: [gmx-users] genion question

2009-08-25 Thread Justin A. Lemkul



Paymon Pirzadeh wrote:

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!



The total charge will undoubtedly fluctuate.  What's most important to look at 
is when you reach the end of a residue and you do not see an integer charge.


-Justin


Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the

No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Re: [gmx-users] genion question

2009-08-25 Thread Paymon Pirzadeh
Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!

Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Thanks for the tips!
> > But I still have problem with my added ion. Justin had told me that ion
> > names are force-field specific! Since I am using OPLSaa, I checked the
> > itp file for Na ion name, and it was Na+. I used this name with the
> 
> No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:
> 
> [ moleculetype ]
> ; molname   nrexcl
> NA+ 1
> 
> [ atoms ]
> ; idat type res nr  residu name at name  cg nr  charge   mass
> 1   opls_4071   NA+ NA   1  1   
> 22.98977
> 
> > -pname switch, but again during the grompp I ran into the following
> > error:
> > Warning: atom name 65870 in AFP_I.top and
> > AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> > 
> > WARNING 1 [file AFP_I.top, line 4151]:
> >   1 non-matching atom name
> >   atom names from AFP_I.top will be used
> >   atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> > 
> > I really do not know what I am doing wrong here! Also regarding past
> > discussions, adding this single ion has lead into the following note:
> >  
> > NOTE 1 [file AFP_I.top, line 4151]:
> >   System has non-zero total charge: 1.00e-02
> > 
> > I am not sure if that much charge will cause me troubles or not!
> > 
> 
> I am somewhat troubled by the magnitude of charge discrepancy.  Look in the 
> .top 
> to see where things start going wrong (i.e., not an integer).  I would think 
> your system would have to be quite large to accumulate such a difference in 
> charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> >> Paymon Pirzadeh wrote:
> >>> Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> >>> negative charge exactly? Does that hurt science or simulation?
> >> It's probably irrelevant. The representation of "decimal" numbers on 
> >> computers can be inexact, such that things like 0.02 added to itself 100 
> >> times does not pass a test for equality with 2. You may be observing 
> >> this kind of thing here. Your protein's [atoms] directive has a running 
> >> count of the total  charge on the molecule - go and read it and see that 
> >> each residue has an integral charge. Hopefully you can observe where the 
> >> rounding error might be occurring and you can make a judgement about 
> >> whether this might be true.
> >>
> >> Mark
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> 

___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Re: [gmx-users] genion question

2009-08-25 Thread Justin A. Lemkul



Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the


No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!



I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php




___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Re: [gmx-users] genion question

2009-08-25 Thread Paymon Pirzadeh
Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the
-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:
  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> > negative charge exactly? Does that hurt science or simulation?
> 
> It's probably irrelevant. The representation of "decimal" numbers on 
> computers can be inexact, such that things like 0.02 added to itself 100 
> times does not pass a test for equality with 2. You may be observing 
> this kind of thing here. Your protein's [atoms] directive has a running 
> count of the total  charge on the molecule - go and read it and see that 
> each residue has an integral charge. Hopefully you can observe where the 
> rounding error might be occurring and you can make a judgement about 
> whether this might be true.
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Re: [gmx-users] genion question

2009-08-25 Thread Mark Abraham

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?


It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Re: [gmx-users] genion question

2009-08-25 Thread Paymon Pirzadeh
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?

Payman 


On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > I realized sth about the previous error message I posted. In the
> > following I have copied the lines (with their line number) which
> > grompp gives warning on! 
> > 
> > 
> > in .gro file:
> > 65868 10940SOLHW265866   5.038   5.739   6.407
> > 65869 10940SOL MW65867   5.103   5.710   6.455
> > 65870 10940SOLLP165868   5.061   5.644   6.524
> > 65871 10940SOLLP265869   5.144   5.630   6.405
> > 65872 10941Na  Na65870   1.844   0.957   1.889
> > 658735.4   6.23500  10.24600
> > 
> > in .top file:
> > 4147 [ molecules ]
> > 4148 ; Compound#mols
> > 4149 Protein_A   1
> > 4150 SOL 10903
> > 4151 Na+  1
> > 
> > I have tested that if I remove the "+" sign, grompp will not work at all
> > and says "such molecule does not exists". 
> > So, I am not sure where the Na-NA mismatch comes from?!
> > 
> 
> Ion names are force field-specific.  If you left -pname as the default, it 
> assigns Na (for ffgmx).  Check ions.itp for the correct name.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> When I look at the .top file generated by pdb2gmx, the last lines show
> >>> how this -0.99 is generated:
> >>>
> >>>442   opls_302 37ARG CZ138   0.64 12.011   ;
> >>> qtot -0.33
> >>>443   opls_300 37ARGNH1139   -0.814.0067   ;
> >>> qtot -1.13
> >>>444   opls_301 37ARG   HH11139   0.46  1.008   ;
> >>> qtot -0.67
> >>>445   opls_301 37ARG   HH12139   0.46  1.008   ;
> >>> qtot -0.21
> >>>446   opls_300 37ARGNH2140   -0.814.0067   ;
> >>> qtot -1.01
> >>>447   opls_301 37ARG   HH21140   0.46  1.008   ;
> >>> qtot -0.55
> >>>448   opls_301 37ARG   HH22140   0.46  1.008   ;
> >>> qtot -0.09
> >>>449   opls_271 37ARG  C1410.7 12.011   ;
> >>> qtot 0.61
> >>>450   opls_272 37ARG O1141   -0.815.9994   ;
> >>> qtot -0.19
> >>>451   opls_272 37ARG O2141   -0.815.9994   ;
> >>> qtot -0.99
> >>>
> >>> The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> >>> simulation is supposed to be close to 7.0, I believe one of the
> >>> negatively-charged side chains needs to be neutralized. That's why I
> >>> think one Na+ might be helpful.
> >>>
> >> That's probably correct.  I just wanted to verify what was in your system. 
> >>  If 
> >> you just had water, it made no sense.  But with a protein involved with 
> >> lots of 
> >> partial charges, these rounding issues do occur.  You really do have a 
> >> system 
> >> with -1 charge.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK! It worked! Thanks a lot again. But I have a final technical
> > question. After running grompp, it shows that my box has a net charge of
> > -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> > OK?! or even this 0.01 charge will cause me troubles?
>  Depending on the size of your system, rounding errors can occur.  It is 
>  unusual 
>  that the hundredths place would be showing this error.  Usually you'd 
>  get 
>  something like 0.8 or something.  Your water topology has a zero net 
>  charge; 
>  is there something else in your system causing the -1 charge?
> 
>  Adding a single Na+ to neutralize the charge may be appropriate, but 
>  that's up 
>  to you based on what's in your system (something else may be broken, but 
>  I just 
>  don't know).
> 
>  -Justin
> 
> > Sorry for tons of e-mails.
> > regards,
> >
> > Payman
> >
> >
> > On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! That's fine. But what if I do not have permissions to make such
> >>> changes in the itp files? Also, isn't that the case that when you 
> >>> define
> >> That's why I said copy the force field files into your local 
> >> directory.  Once 
> >> there, you can modify them.
> >>
> >>> sth for the second time, grompp will take the second one? Sorry for 
> >>> mass
> >>> of e-mail!
> >>>
> >> That is only true in the case of .mdp files.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > I have done that already! I use my local copy

Re: [gmx-users] genion question

2006-12-11 Thread Mark Abraham
> Hi Guys,
>
>
>
> I have a question.  I am using genion to add two ZN2+ ions to a protein
> that
> already has two.  I thought I would just use genion with –np 2.  However
> it
> seemed to recognize that there were already two in the file and added
> none.
> So instead I used the parameter –np 4.  This seemed to add two, for a
> total
> of four, which I wanted.  However sometimes it seems to add two too many!
> Am I understanding the proper use of the –np parameter?

If it "seemed" to add two too many, then the most likely cause was that
you had fewer ions in your input structure than you thought you had. You
should check out the man page for genion, and consider using -pq.

Mark

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php