Re: [gmx-users] question

2017-12-29 Thread s.ghasemlou 
در 2017-12-30 10:31، Nikhil Maroli نوشته است:

> Hello,
> 
> Read the previous posts and do a google search. maybe you can start from
> here :
> 
> http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist

Thank you dear Nikhil Maroli for your response. I have read the posts
before and also visited the site you introduced but it didn't help me.
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Re: [gmx-users] question

2017-12-29 Thread s.ghasemlou 
در 2017-12-30 10:15، RAHUL SURESH نوشته است:

> On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou  wrote: 
> thanks for your response 
> 
>> Hello every one,
>> 
>> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
>> topol.top -o ions.tpr" I get the error:
>> 
>> ERROR 1 [file topol.top, line 863]:
>> ERROR: The cut-off length is longer than half the shortest box vector
>> or
>> longer than the smallest box diagonal element. Increase the box size
>> or
>> decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)
> 
> What is the cut off scheme and value..? 
> 
> below is the em.mdp file content I have used 
> 
> ; LINES STARTING WITH ';' ARE COMMENTS
> title  = Minimization ; Title of run 
> ; Parameters describing what to do, when to stop and what to save
> 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
> 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 (yes/no) 
> 
>> I have tried different rlist, r columb and rvdw values. I have also
>> changed the box vector several times, but I still get the same error. I
>> don't know how to change them to fix the error.
>> 
>> There is also the below warning:
>> 
>> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
>> - OW)
>> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
>> HW1)
>> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
>> - HW2)
>> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
>> - OW)
>> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
>> HW1)
>> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
>> - HW2)
>> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
>> - OW)
>> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
>> - HW1)
>> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
>> - HW2)
>> Warning: atom name 10 in topol.top and totalbox1.gro does not match
>> (H110 - OW)
>> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
>> - HW1)
>> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
>> - HW2)
>> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
>> - OW)
>> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
>> - HW1)
>> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
>> - HW2)
>> Warning: atom name 16 in topol.top and totalbox1.gro does not match
>> (H100 - OW)
>> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
>> - HW1)
>> Warning: atom name 18 in topol.top and totalbox1.gro does not match
>> (H102 - HW2)
>> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
>> - OW)
>> Warning: atom name 20 in topol.top and totalbox1.gro does not match
>> (H101 - HW1)
>> (more than 20 non-matching atom names)
>> WARNING 1 [file topol.top, line 863]:
>> 32798 non-matching atom names
>> atom names from topol.top will be used
>> atom names from totalbox1.gro will be ignored
> 
> You can use maxwarn flag or change the cane in toolbox.gro 
> would you please tell me what the cane is in a .gro file? because using 
> maxwarn flag didn't fix it.
> 
>> As I checked both the .gro and topol.top contents, atom names are the
>> same but here atom names of solvent water are mixed with atom names of
>> the ligand I used.
> 
> Someone else would definitely help you in This.
> 
>> please help me on this. Thanks in advance.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> -- 
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] question

2017-12-29 Thread Nikhil Maroli 
Hello,

Read the previous posts and do a google search. maybe you can start from
here :

http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist
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Re: [gmx-users] Issue regarding MN+2

2017-12-29 Thread RAHUL SURESH 
Yup.. they are available.. literature should help in that.

On Sat, 30 Dec 2017 at 10:53 AM, Amir Zeb  wrote:

> Alright Dr. Justin,
>
> Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
> you haven't included in the port?
> I'm searching the literature too to find something worthy.
>
> Thanks!
>
> ~Amir
>
> On Fri, Dec 29, 2017 at 8:17 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/29/17 10:39 AM, Amir Zeb wrote:
> >
> >> Thanks Dr. Justin.
> >>
> >> I didn't add this stuff by my own.
> >> I have created Mn+2 topology by simple pdb2gmx command.
> >>
> >
> > Someone hacked your files and added it at some point. None of the
> releases
> > of the C36 port that I have ever made had contained Mn2+ parameters.
> There
> > are CHARMM-compatible parameters that could be added as part of a larger
> > metal parameter set, but they've never been included in the port.
> >
> > Regardless, that's what you need to do - add the correct sigma and
> epsilon
> > values to ffnonbonded.itp for the MN atom type.
> >
> > -Justin
> >
> >
> > ~Amir
> >>
> >> On Dec 30, 2017 12:21 AM, "Justin Lemkul"  wrote:
> >>
> >>
> >>> On 12/29/17 10:11 AM, Amir Zeb wrote:
> >>>
> >>> Hello dear gromacs users,
> 
>  I want to simulate a protein which has two Mn+2 ions as co-factor.
>  Till the solvation, I could prepare the system, but at neutralization
>  step,
>  grompp gives me this fatal error.
> 
>  Fatal error:
>  Atomtype MN not found
> 
>  My system has this topology for Mn+2:
> 
>  [ moleculetype ]
>  ; Namenrexcl
>  Other_chain_C2  3
> 
>  [ atoms ]
>  ;   nr   type  resnr residue  atom   cgnr charge   mass
>  typeB
>  chargeB  massB
>  ; residue 501 MN2  rtp MN   q +2.0
> 1MN 501MN2  MN  1  2  54.94
>   ;
>  qtot 2
>  ; residue 502 MN2  rtp MN   q +2.0
> 2MN 502MN2  MN  2  2  54.94
>   ;
>  qtot 4
> 
> 
>  And the Mn+2 has this configuration:
> 
>  501MN2 MN 4551   5.405   5.564   2.987
>  502MN2 MN 4552   5.582   5.590   3.497
> 
>  I have used Charmm36 ff, and the gromacs version is 5.0.6
> 
>  Please let me know how can I fix this issue?
> 
>  This is not a standard CHARMM atom type - did you add it yourself? If
> >>> so,
> >>> what was the source of the parameters? It looks like you have a residue
> >>> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
> >>> actually have parameters assigned for the atom type in ffnonbonded.itp.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Assistant Professor
> >>> Virginia Tech Department of Biochemistry
> >>>
> >>> 303 Engel Hall
> >>> 340 West Campus Dr.
> >>> Blacksburg, VA 24061
> >>>
> >>> jalem...@vt.edu | (540) 231-3129
> >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>>
> >>> ==
> >>>
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/Support
> >>> /Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>> * 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.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * 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.
> >
> --
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> * Please search the archive at
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] question

2017-12-29 Thread RAHUL SURESH 
On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou  wrote:

> Hello every one,
>
> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> topol.top -o ions.tpr" I get the error:
>
> ERROR 1 [file topol.top, line 863]:
>   ERROR: The cut-off length is longer than half the shortest box vector
> or
>   longer than the smallest box diagonal element. Increase the box size
> or
>   decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)

What is the cut off scheme and value..?

>
>
> I have tried different rlist, r columb and rvdw values. I have also
> changed the box vector several times, but I still get the same error. I
> don't know how to change them to fix the error.
>
> There is also the below warning:
>
> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> - OW)
> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
> HW1)
> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> - HW2)
> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> - OW)
> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
> HW1)
> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> - HW2)
> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> - OW)
> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> - HW1)
> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
> - HW2)
> Warning: atom name 10 in topol.top and totalbox1.gro does not match
> (H110 - OW)
> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
> - HW1)
> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
> - HW2)
> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
> - OW)
> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
> - HW1)
> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
> - HW2)
> Warning: atom name 16 in topol.top and totalbox1.gro does not match
> (H100 - OW)
> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
> - HW1)
> Warning: atom name 18 in topol.top and totalbox1.gro does not match
> (H102 - HW2)
> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
> - OW)
> Warning: atom name 20 in topol.top and totalbox1.gro does not match
> (H101 - HW1)
> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 863]:
>   32798 non-matching atom names
>   atom names from topol.top will be used
>   atom names from totalbox1.gro will be ignored

You can use maxwarn flag or change the cane in toolbox.gro

>
>
> As I checked both the .gro and topol.top contents, atom names are the
> same but here atom names of solvent water are mixed with atom names of
> the ligand I used.

Someone else would definitely help you in This.

>
> please help me on this. Thanks in advance.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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[gmx-users] question

2017-12-29 Thread s.ghasemlou 
Hello every one, 

After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
topol.top -o ions.tpr" I get the error: 

ERROR 1 [file topol.top, line 863]:
  ERROR: The cut-off length is longer than half the shortest box vector
or
  longer than the smallest box diagonal element. Increase the box size
or
  decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343) 

I have tried different rlist, r columb and rvdw values. I have also
changed the box vector several times, but I still get the same error. I
don't know how to change them to fix the error. 

There is also the below warning:

Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
- OW)
Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
HW1)
Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
- HW2)
Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
- OW)
Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
HW1)
Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
- HW2)
Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
- OW)
Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
- HW1)
Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
- HW2)
Warning: atom name 10 in topol.top and totalbox1.gro does not match
(H110 - OW)
Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
- HW1)
Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
- HW2)
Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
- OW)
Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
- HW1)
Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
- HW2)
Warning: atom name 16 in topol.top and totalbox1.gro does not match
(H100 - OW)
Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
- HW1)
Warning: atom name 18 in topol.top and totalbox1.gro does not match
(H102 - HW2)
Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
- OW)
Warning: atom name 20 in topol.top and totalbox1.gro does not match
(H101 - HW1)
(more than 20 non-matching atom names) 
WARNING 1 [file topol.top, line 863]:
  32798 non-matching atom names
  atom names from topol.top will be used
  atom names from totalbox1.gro will be ignored 

As I checked both the .gro and topol.top contents, atom names are the
same but here atom names of solvent water are mixed with atom names of
the ligand I used. 
please help me on this. Thanks in advance.
-- 
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Re: [gmx-users] Issue regarding MN+2

2017-12-29 Thread Amir Zeb 
Alright Dr. Justin,

Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
you haven't included in the port?
I'm searching the literature too to find something worthy.

Thanks!

~Amir

On Fri, Dec 29, 2017 at 8:17 AM, Justin Lemkul  wrote:

>
>
> On 12/29/17 10:39 AM, Amir Zeb wrote:
>
>> Thanks Dr. Justin.
>>
>> I didn't add this stuff by my own.
>> I have created Mn+2 topology by simple pdb2gmx command.
>>
>
> Someone hacked your files and added it at some point. None of the releases
> of the C36 port that I have ever made had contained Mn2+ parameters. There
> are CHARMM-compatible parameters that could be added as part of a larger
> metal parameter set, but they've never been included in the port.
>
> Regardless, that's what you need to do - add the correct sigma and epsilon
> values to ffnonbonded.itp for the MN atom type.
>
> -Justin
>
>
> ~Amir
>>
>> On Dec 30, 2017 12:21 AM, "Justin Lemkul"  wrote:
>>
>>
>>> On 12/29/17 10:11 AM, Amir Zeb wrote:
>>>
>>> Hello dear gromacs users,

 I want to simulate a protein which has two Mn+2 ions as co-factor.
 Till the solvation, I could prepare the system, but at neutralization
 step,
 grompp gives me this fatal error.

 Fatal error:
 Atomtype MN not found

 My system has this topology for Mn+2:

 [ moleculetype ]
 ; Namenrexcl
 Other_chain_C2  3

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass
 typeB
 chargeB  massB
 ; residue 501 MN2  rtp MN   q +2.0
1MN 501MN2  MN  1  2  54.94
  ;
 qtot 2
 ; residue 502 MN2  rtp MN   q +2.0
2MN 502MN2  MN  2  2  54.94
  ;
 qtot 4


 And the Mn+2 has this configuration:

 501MN2 MN 4551   5.405   5.564   2.987
 502MN2 MN 4552   5.582   5.590   3.497

 I have used Charmm36 ff, and the gromacs version is 5.0.6

 Please let me know how can I fix this issue?

 This is not a standard CHARMM atom type - did you add it yourself? If
>>> so,
>>> what was the source of the parameters? It looks like you have a residue
>>> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
>>> actually have parameters assigned for the atom type in ffnonbonded.itp.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * 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.
>
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Re: [gmx-users] Problems with Energy Minimization in Solvated Ligand

2017-12-29 Thread Billy Williams-Noonan 
Hi Toan,

There is probably either something wrong with your topology or the initial
geometry of your system is somehow wrong.  How did you paramaterise your
system?

Cheers,

Billy

On 30 December 2017 at 12:39, Toan Nguyen  wrote:

> So I believe I solved my problem by changing to:
> couple-intramol = yes
> in my enmin.00.mdp file.
>
> However, looking at the gromacs manual
> , changing the
> couple-intramol to "yes"  means that:
>
> "The intra-molecular Van der Waals and Coulomb interactions are also turned
> on/off. This can be useful for partitioning free-energies of relatively
> large molecules, where the intra-molecular non-bonded interactions might
> lead to kinetically trapped vacuum conformations. The 1-4 pair interactions
> are not turned off."
>
> In your tutorial
>  gmx-tutorials/complex/04_ions.html>,
> the provided mdp file has couple-intramol = 0.
> Would making the above changes affect my analysis if I intend to do an MBAR
> (Multi-state Bennett Acceptance Ratio) analysis?
>
> On Fri, Dec 29, 2017 at 2:42 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/29/17 5:14 PM, Toan Nguyen wrote:
> >
> >> Is it okay to see this same warning when running npt and nvt?
> >>
> >
> > No, hence the "IMPORTANT" part of the message. Your system is unstable
> and
> > you should diagnose why.
> >
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> > Diagnosing_an_Unstable_System
> >
> > -Justin
> >
> > "*WARNING: Listed nonbonded interaction between particles 1 and 119*
> >> *at distance 2.103 which is larger than the table limit 2.000 nm.*
> >>
> >> *This is likely either a 1,4 interaction, or a listed interaction
> inside*
> >> *a smaller molecule you are decoupling during a free energy
> calculation.*
> >> *Since interactions at distances beyond the table cannot be computed,*
> >> *they are skipped until they are inside the table limit again. You will*
> >> *only see this message once, even if it occurs for several
> interactions.*
> >>
> >> *IMPORTANT: This should not happen in a stable simulation, so there is*
> >> *probably something wrong with your system. Only change the
> >> table-extension*
> >> *distance in the mdp file if you are really sure that is the reason."*
> >>
> >> On Thu, Dec 28, 2017 at 6:38 PM, Justin Lemkul  wrote:
> >>
> >>
> >>> On 12/28/17 9:36 PM, Toan Nguyen wrote:
> >>>
> >>> How would we go about doing another energy minimization? I realized I
>  sent
> 
>  Double precision, or using conjugate gradients, or using steepest
> >>> descents
> >>> with a smaller initial step.
> >>>
> >>> the wrong tutorial earlier, I was actually following this one Absolute
> >>>
>  Binding Free Energy - Gromacs 2016
>    y_-_Gromacs_2016>
>  by David Mobley.
> 
>  Good luck getting that to converge with a peptide :)
> >>>
> >>> -Justin
> >>>
> >>>
> >>> On Thu, Dec 28, 2017 at 6:30 PM, Justin Lemkul 
> wrote:
> >>>
> 
>  On 12/28/17 8:40 PM, Toan Nguyen wrote:
> >
> > Hi,
> >
> >> I am currently following the Gromacs Tutorial by Bevan Lab (Link
> >>  >> x-tutorials/complex/05_EM.html>)
> >> to run a simulation on a ligand from the 1mnb protein. However, I am
> >> running into issues with the energy minimization step where I run
> *gmx
> >> mdrun -v -nt 1 -deffnm em*, but an error arises saying,
> >>
> >> *"WARNING: Listed nonbonded interaction between particles 1 and 119*
> >> *at distance 2.108 which is larger than the table limit 2.000 nm.*
> >>
> >> *This is likely either a 1,4 interaction, or a listed interaction
> >> inside*
> >> *a smaller molecule you are decoupling during a free energy
> >> calculation.*
> >> *Since interactions at distances beyond the table cannot be
> computed,*
> >> *they are skipped until they are inside the table limit again. You
> >> will*
> >> *only see this message once, even if it occurs for several
> >> interactions.*
> >>
> >> *IMPORTANT: This should not happen in a stable simulation, so there
> >> is*
> >> *probably something wrong with your system. Only change the
> >> table-extension*
> >> *distance in the mdp file if you are really sure that is the
> reason."*
> >>
> >> and then energy minimization runs for ~120 steps before saying,
> >>
> >> *"Energy minimization has stopped, but the forces have not converged
> >> to
> >> the*
> >> *requested precision Fmax < 100 (which may not be possible for your
> >> system).*
> >> *It stopped because the algorithm tried to make a new step whose
> size
> >> was
> >> too*
> >> *small, or there was no change in the energy since last step. Either
> >> way,
> >> we*
>

Re: [gmx-users] Problems with Energy Minimization in Solvated Ligand

2017-12-29 Thread Toan Nguyen 
So I believe I solved my problem by changing to:
couple-intramol = yes
in my enmin.00.mdp file.

However, looking at the gromacs manual
, changing the
couple-intramol to "yes"  means that:

"The intra-molecular Van der Waals and Coulomb interactions are also turned
on/off. This can be useful for partitioning free-energies of relatively
large molecules, where the intra-molecular non-bonded interactions might
lead to kinetically trapped vacuum conformations. The 1-4 pair interactions
are not turned off."

In your tutorial
,
the provided mdp file has couple-intramol = 0.
Would making the above changes affect my analysis if I intend to do an MBAR
(Multi-state Bennett Acceptance Ratio) analysis?

On Fri, Dec 29, 2017 at 2:42 PM, Justin Lemkul  wrote:

>
>
> On 12/29/17 5:14 PM, Toan Nguyen wrote:
>
>> Is it okay to see this same warning when running npt and nvt?
>>
>
> No, hence the "IMPORTANT" part of the message. Your system is unstable and
> you should diagnose why.
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System
>
> -Justin
>
> "*WARNING: Listed nonbonded interaction between particles 1 and 119*
>> *at distance 2.103 which is larger than the table limit 2.000 nm.*
>>
>> *This is likely either a 1,4 interaction, or a listed interaction inside*
>> *a smaller molecule you are decoupling during a free energy calculation.*
>> *Since interactions at distances beyond the table cannot be computed,*
>> *they are skipped until they are inside the table limit again. You will*
>> *only see this message once, even if it occurs for several interactions.*
>>
>> *IMPORTANT: This should not happen in a stable simulation, so there is*
>> *probably something wrong with your system. Only change the
>> table-extension*
>> *distance in the mdp file if you are really sure that is the reason."*
>>
>> On Thu, Dec 28, 2017 at 6:38 PM, Justin Lemkul  wrote:
>>
>>
>>> On 12/28/17 9:36 PM, Toan Nguyen wrote:
>>>
>>> How would we go about doing another energy minimization? I realized I
 sent

 Double precision, or using conjugate gradients, or using steepest
>>> descents
>>> with a smaller initial step.
>>>
>>> the wrong tutorial earlier, I was actually following this one Absolute
>>>
 Binding Free Energy - Gromacs 2016
 
 by David Mobley.

 Good luck getting that to converge with a peptide :)
>>>
>>> -Justin
>>>
>>>
>>> On Thu, Dec 28, 2017 at 6:30 PM, Justin Lemkul  wrote:
>>>

 On 12/28/17 8:40 PM, Toan Nguyen wrote:
>
> Hi,
>
>> I am currently following the Gromacs Tutorial by Bevan Lab (Link
>> > x-tutorials/complex/05_EM.html>)
>> to run a simulation on a ligand from the 1mnb protein. However, I am
>> running into issues with the energy minimization step where I run *gmx
>> mdrun -v -nt 1 -deffnm em*, but an error arises saying,
>>
>> *"WARNING: Listed nonbonded interaction between particles 1 and 119*
>> *at distance 2.108 which is larger than the table limit 2.000 nm.*
>>
>> *This is likely either a 1,4 interaction, or a listed interaction
>> inside*
>> *a smaller molecule you are decoupling during a free energy
>> calculation.*
>> *Since interactions at distances beyond the table cannot be computed,*
>> *they are skipped until they are inside the table limit again. You
>> will*
>> *only see this message once, even if it occurs for several
>> interactions.*
>>
>> *IMPORTANT: This should not happen in a stable simulation, so there
>> is*
>> *probably something wrong with your system. Only change the
>> table-extension*
>> *distance in the mdp file if you are really sure that is the reason."*
>>
>> and then energy minimization runs for ~120 steps before saying,
>>
>> *"Energy minimization has stopped, but the forces have not converged
>> to
>> the*
>> *requested precision Fmax < 100 (which may not be possible for your
>> system).*
>> *It stopped because the algorithm tried to make a new step whose size
>> was
>> too*
>> *small, or there was no change in the energy since last step. Either
>> way,
>> we*
>> *regard the minimization as converged to within the available machine*
>> *precision, given your starting configuration and EM parameters.*
>>
>> *Double precision normally gives you higher accuracy, but this is
>> often
>> not*
>> *needed for preparing to run molecular dynamics.*
>>
>> *writing lowest energy coordinates.*
>>
>> *Steepest Descents converged to machine precision in 94 steps,*
>> *but did not reach the requested Fmax < 100.*

[gmx-users] How do I calculate per-atom per-frame SASA?

2017-12-29 Thread Denny Bromley 
Hi all,

I apologize for the newbie question, but the google machine is failing me.
I am currently outputting the per-frame SASA as well as the per-atom
mean+-stdev, but what I would like is per-atom per-frame sasa.  Is this
possible? Gromacs must be touching those values in order to calculate mean
and stdev, I just want it to save them out.

Thanks!
-denny-
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[gmx-users] lipid bilayer simulation-simulation setup

2017-12-29 Thread Mohsen Ramezanpour 
Hi Everyone,

Lipid bilayers are (almost all the times) simulated in a rectangular or
cubic boxes where all the angles are 90 between the PBC box sides. They are
usually equilibrated with semi-isotropic Berendsen P-coupling whereas the
production runs use semi-isotropic Parrinello-Rahman p-coupling (this part
make sense). I have two questions:

1) What is the problem if we use a triclinic box with 90 90 120 angles for
bilayer simulation:
If we choose the z-direction as the normal vector to the bilayer. and a
semi-isotropic p-coupling will be applied to the XY plane?


2) There are some publications who used the Berendsen coupling for
production run as well. They do not usually explain why they prefer this
barostat for the production run. It is known that Berendsen barostat is not
producing the target ensemble as good as Parrinello-Rahman.
It might be, however, because of using anisotropic p-coupling where both
the box sides lengths and angles are allowed to change.

Any idea?
Thanks in advance for your input on this questions.

Cheers,
Mohsen

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Re: [gmx-users] Problems with Energy Minimization in Solvated Ligand

2017-12-29 Thread Justin Lemkul 



On 12/29/17 5:14 PM, Toan Nguyen wrote:

Is it okay to see this same warning when running npt and nvt?


No, hence the "IMPORTANT" part of the message. Your system is unstable 
and you should diagnose why.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin


"*WARNING: Listed nonbonded interaction between particles 1 and 119*
*at distance 2.103 which is larger than the table limit 2.000 nm.*

*This is likely either a 1,4 interaction, or a listed interaction inside*
*a smaller molecule you are decoupling during a free energy calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the table-extension*
*distance in the mdp file if you are really sure that is the reason."*

On Thu, Dec 28, 2017 at 6:38 PM, Justin Lemkul  wrote:



On 12/28/17 9:36 PM, Toan Nguyen wrote:


How would we go about doing another energy minimization? I realized I sent


Double precision, or using conjugate gradients, or using steepest descents
with a smaller initial step.

the wrong tutorial earlier, I was actually following this one Absolute

Binding Free Energy - Gromacs 2016

by David Mobley.


Good luck getting that to converge with a peptide :)

-Justin


On Thu, Dec 28, 2017 at 6:30 PM, Justin Lemkul  wrote:



On 12/28/17 8:40 PM, Toan Nguyen wrote:

Hi,

I am currently following the Gromacs Tutorial by Bevan Lab (Link
)
to run a simulation on a ligand from the 1mnb protein. However, I am
running into issues with the energy minimization step where I run *gmx
mdrun -v -nt 1 -deffnm em*, but an error arises saying,

*"WARNING: Listed nonbonded interaction between particles 1 and 119*
*at distance 2.108 which is larger than the table limit 2.000 nm.*

*This is likely either a 1,4 interaction, or a listed interaction
inside*
*a smaller molecule you are decoupling during a free energy
calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several
interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the
table-extension*
*distance in the mdp file if you are really sure that is the reason."*

and then energy minimization runs for ~120 steps before saying,

*"Energy minimization has stopped, but the forces have not converged to
the*
*requested precision Fmax < 100 (which may not be possible for your
system).*
*It stopped because the algorithm tried to make a new step whose size
was
too*
*small, or there was no change in the energy since last step. Either
way,
we*
*regard the minimization as converged to within the available machine*
*precision, given your starting configuration and EM parameters.*

*Double precision normally gives you higher accuracy, but this is often
not*
*needed for preparing to run molecular dynamics.*

*writing lowest energy coordinates.*

*Steepest Descents converged to machine precision in 94 steps,*
*but did not reach the requested Fmax < 100.*
*Potential Energy  = -1.4016720e+05*
*Maximum force =  1.9569155e+03 on atom 259*
*Norm of force =  9.6724640e+01"*

When I do the tutorial with the provided input files, this message does
not
show up and the energy minimization reaches 500+ steps. How can I fix my
input files so that the energy minimization does not run into the
problem
above?

Below is the link to my input files:
Link


The messages above just indicate you probably have a bad contact

somewhere
early on in the minimization process. If EM finishes (which it does),
then
the bad contact has been at least somewhat resolved. The forces are still
somewhat high, so you will likely need additional minimization and/or
double precision, as the message from mdrun suggests.

The protein-ligand complex tutorial isn't really relevant here; you just
have a very simple protein in water, not that it makes much difference.
But
don't get too hung up on having a "ligand" in your system. You have a
peptide, so it's nothing that requires any really special procedur

e.

-Justin

--
==

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

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

jalem...@

Re: [gmx-users] Problems with Energy Minimization in Solvated Ligand

2017-12-29 Thread Toan Nguyen 
Is it okay to see this same warning when running npt and nvt?

"*WARNING: Listed nonbonded interaction between particles 1 and 119*
*at distance 2.103 which is larger than the table limit 2.000 nm.*

*This is likely either a 1,4 interaction, or a listed interaction inside*
*a smaller molecule you are decoupling during a free energy calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the table-extension*
*distance in the mdp file if you are really sure that is the reason."*

On Thu, Dec 28, 2017 at 6:38 PM, Justin Lemkul  wrote:

>
>
> On 12/28/17 9:36 PM, Toan Nguyen wrote:
>
>> How would we go about doing another energy minimization? I realized I sent
>>
>
> Double precision, or using conjugate gradients, or using steepest descents
> with a smaller initial step.
>
> the wrong tutorial earlier, I was actually following this one Absolute
>> Binding Free Energy - Gromacs 2016
>> > y_-_Gromacs_2016>
>> by David Mobley.
>>
>
> Good luck getting that to converge with a peptide :)
>
> -Justin
>
>
> On Thu, Dec 28, 2017 at 6:30 PM, Justin Lemkul  wrote:
>>
>>
>>> On 12/28/17 8:40 PM, Toan Nguyen wrote:
>>>
>>> Hi,

 I am currently following the Gromacs Tutorial by Bevan Lab (Link
 )
 to run a simulation on a ligand from the 1mnb protein. However, I am
 running into issues with the energy minimization step where I run *gmx
 mdrun -v -nt 1 -deffnm em*, but an error arises saying,

 *"WARNING: Listed nonbonded interaction between particles 1 and 119*
 *at distance 2.108 which is larger than the table limit 2.000 nm.*

 *This is likely either a 1,4 interaction, or a listed interaction
 inside*
 *a smaller molecule you are decoupling during a free energy
 calculation.*
 *Since interactions at distances beyond the table cannot be computed,*
 *they are skipped until they are inside the table limit again. You will*
 *only see this message once, even if it occurs for several
 interactions.*

 *IMPORTANT: This should not happen in a stable simulation, so there is*
 *probably something wrong with your system. Only change the
 table-extension*
 *distance in the mdp file if you are really sure that is the reason."*

 and then energy minimization runs for ~120 steps before saying,

 *"Energy minimization has stopped, but the forces have not converged to
 the*
 *requested precision Fmax < 100 (which may not be possible for your
 system).*
 *It stopped because the algorithm tried to make a new step whose size
 was
 too*
 *small, or there was no change in the energy since last step. Either
 way,
 we*
 *regard the minimization as converged to within the available machine*
 *precision, given your starting configuration and EM parameters.*

 *Double precision normally gives you higher accuracy, but this is often
 not*
 *needed for preparing to run molecular dynamics.*

 *writing lowest energy coordinates.*

 *Steepest Descents converged to machine precision in 94 steps,*
 *but did not reach the requested Fmax < 100.*
 *Potential Energy  = -1.4016720e+05*
 *Maximum force =  1.9569155e+03 on atom 259*
 *Norm of force =  9.6724640e+01"*

 When I do the tutorial with the provided input files, this message does
 not
 show up and the energy minimization reaches 500+ steps. How can I fix my
 input files so that the energy minimization does not run into the
 problem
 above?

 Below is the link to my input files:
 Link
 

 The messages above just indicate you probably have a bad contact
>>> somewhere
>>> early on in the minimization process. If EM finishes (which it does),
>>> then
>>> the bad contact has been at least somewhat resolved. The forces are still
>>> somewhat high, so you will likely need additional minimization and/or
>>> double precision, as the message from mdrun suggests.
>>>
>>> The protein-ligand complex tutorial isn't really relevant here; you just
>>> have a very simple protein in water, not that it makes much difference.
>>> But
>>> don't get too hung up on having a "ligand" in your system. You have a
>>> peptide, so it's nothing that requires any really special procedur
>>> 
>>> e.
>>>
>>> -Justin
>>>
>>> --
>>> ==

Re: [gmx-users] Issue regarding MN+2

2017-12-29 Thread Justin Lemkul 



On 12/29/17 10:39 AM, Amir Zeb wrote:

Thanks Dr. Justin.

I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.


Someone hacked your files and added it at some point. None of the 
releases of the C36 port that I have ever made had contained Mn2+ 
parameters. There are CHARMM-compatible parameters that could be added 
as part of a larger metal parameter set, but they've never been included 
in the port.


Regardless, that's what you need to do - add the correct sigma and 
epsilon values to ffnonbonded.itp for the MN atom type.


-Justin


~Amir

On Dec 30, 2017 12:21 AM, "Justin Lemkul"  wrote:



On 12/29/17 10:11 AM, Amir Zeb wrote:


Hello dear gromacs users,

I want to simulate a protein which has two Mn+2 ions as co-factor.
Till the solvation, I could prepare the system, but at neutralization
step,
grompp gives me this fatal error.

Fatal error:
Atomtype MN not found

My system has this topology for Mn+2:

[ moleculetype ]
; Namenrexcl
Other_chain_C2  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
; residue 501 MN2  rtp MN   q +2.0
   1MN 501MN2  MN  1  2  54.94   ;
qtot 2
; residue 502 MN2  rtp MN   q +2.0
   2MN 502MN2  MN  2  2  54.94   ;
qtot 4


And the Mn+2 has this configuration:

501MN2 MN 4551   5.405   5.564   2.987
502MN2 MN 4552   5.582   5.590   3.497

I have used Charmm36 ff, and the gromacs version is 5.0.6

Please let me know how can I fix this issue?


This is not a standard CHARMM atom type - did you add it yourself? If so,
what was the source of the parameters? It looks like you have a residue
defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
actually have parameters assigned for the atom type in ffnonbonded.itp.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Issue regarding MN+2

2017-12-29 Thread Amir Zeb 
Thanks Dr. Justin.

I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.

~Amir

On Dec 30, 2017 12:21 AM, "Justin Lemkul"  wrote:

>
>
> On 12/29/17 10:11 AM, Amir Zeb wrote:
>
>> Hello dear gromacs users,
>>
>> I want to simulate a protein which has two Mn+2 ions as co-factor.
>> Till the solvation, I could prepare the system, but at neutralization
>> step,
>> grompp gives me this fatal error.
>>
>> Fatal error:
>> Atomtype MN not found
>>
>> My system has this topology for Mn+2:
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Other_chain_C2  3
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
>>chargeB  massB
>> ; residue 501 MN2  rtp MN   q +2.0
>>   1MN 501MN2  MN  1  2  54.94   ;
>> qtot 2
>> ; residue 502 MN2  rtp MN   q +2.0
>>   2MN 502MN2  MN  2  2  54.94   ;
>> qtot 4
>>
>>
>> And the Mn+2 has this configuration:
>>
>>501MN2 MN 4551   5.405   5.564   2.987
>>502MN2 MN 4552   5.582   5.590   3.497
>>
>> I have used Charmm36 ff, and the gromacs version is 5.0.6
>>
>> Please let me know how can I fix this issue?
>>
>
> This is not a standard CHARMM atom type - did you add it yourself? If so,
> what was the source of the parameters? It looks like you have a residue
> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
> actually have parameters assigned for the atom type in ffnonbonded.itp.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Issue regarding MN+2

2017-12-29 Thread Justin Lemkul 



On 12/29/17 10:11 AM, Amir Zeb wrote:

Hello dear gromacs users,

I want to simulate a protein which has two Mn+2 ions as co-factor.
Till the solvation, I could prepare the system, but at neutralization step,
grompp gives me this fatal error.

Fatal error:
Atomtype MN not found

My system has this topology for Mn+2:

[ moleculetype ]
; Namenrexcl
Other_chain_C2  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
; residue 501 MN2  rtp MN   q +2.0
  1MN 501MN2  MN  1  2  54.94   ;
qtot 2
; residue 502 MN2  rtp MN   q +2.0
  2MN 502MN2  MN  2  2  54.94   ;
qtot 4


And the Mn+2 has this configuration:

   501MN2 MN 4551   5.405   5.564   2.987
   502MN2 MN 4552   5.582   5.590   3.497

I have used Charmm36 ff, and the gromacs version is 5.0.6

Please let me know how can I fix this issue?


This is not a standard CHARMM atom type - did you add it yourself? If 
so, what was the source of the parameters? It looks like you have a 
residue defined in the .rtp, hence pdb2gmx wrote the topology, but you 
don't actually have parameters assigned for the atom type in 
ffnonbonded.itp.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Issue regarding MN+2

2017-12-29 Thread Amir Zeb 
Hello dear gromacs users,

I want to simulate a protein which has two Mn+2 ions as co-factor.
Till the solvation, I could prepare the system, but at neutralization step,
grompp gives me this fatal error.

Fatal error:
Atomtype MN not found

My system has this topology for Mn+2:

[ moleculetype ]
; Namenrexcl
Other_chain_C2  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB
; residue 501 MN2  rtp MN   q +2.0
 1MN 501MN2  MN  1  2  54.94   ;
qtot 2
; residue 502 MN2  rtp MN   q +2.0
 2MN 502MN2  MN  2  2  54.94   ;
qtot 4


And the Mn+2 has this configuration:

  501MN2 MN 4551   5.405   5.564   2.987
  502MN2 MN 4552   5.582   5.590   3.497

I have used Charmm36 ff, and the gromacs version is 5.0.6

Please let me know how can I fix this issue?

~Amir
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Re: [gmx-users] Regarding finding a ion/molecule in forecefield

2017-12-29 Thread Justin Lemkul 



On 12/29/17 8:25 AM, Dilip H N wrote:

1] I wanted carbonate ion with -2 ion charge. (i checked in atomtypes.atp
where, carbonate  is mentioned as "CG2O6 12.01100 ; carbonyl C: urea,
carbonate",  "OG2D2  15.99940 ; carbonyl O: negative groups: carboxylates,
carbonate").


Nothing in the .atp file is useful here. What I told you is what you 
wanted, the CO3 residue (in the merged.rtp file) has a -2 charge.



And i also checked with ions.itp (in which the ions are represented), but i
could find only calcium with +2 charge and not carbonate ion. (hope while
converting from gmx pdb2gmx is it converted into an ion ..??)


pdb2gmx never reads ions.itp - it reads .rtp files. You'll find both 
species there.



2] In general how can i find/search for the required molecule and in which
forcefield is it present in...?


You have to go to the source force field files. GROMACS files don't give 
you any information about what residues are; they assume you know. If 
you download the CHARMM36 tarball from the MacKerell website and in the 
toppar directory, issue:


grep -ri "carbonate" * | grep RESI

you will find what you need. Then just check that the same residues are 
defined in the GROMACS .rtp file and proceed.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Regarding finding a ion/molecule in forecefield

2017-12-29 Thread Dilip H N 
1] I wanted carbonate ion with -2 ion charge. (i checked in atomtypes.atp
where, carbonate  is mentioned as "CG2O6 12.01100 ; carbonyl C: urea,
carbonate",  "OG2D2  15.99940 ; carbonyl O: negative groups: carboxylates,
carbonate").
And i also checked with ions.itp (in which the ions are represented), but i
could find only calcium with +2 charge and not carbonate ion. (hope while
converting from gmx pdb2gmx is it converted into an ion ..??)

2] In general how can i find/search for the required molecule and in which
forcefield is it present in...?

Thank you.




‌

On Fri, Dec 29, 2017 at 6:19 PM, Justin Lemkul  wrote:

>
>
> On 12/29/17 7:43 AM, Dilip H N wrote:
>
>> Hello all,
>> How to find out/search a specific molecule or ion is present in which
>> forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
>> molecule), and hence can generate .pdb file corresponding to that residue
>> naming in the FF and generate its topology.
>>
>> In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
>> which forcefield is it present.
>>
>> Any suggestions...
>>
>
> Both are in CHARMM36. Ca2+ is CAL and carbonate is CO3.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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> Gromacs Users mailing list
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding finding a ion/molecule in forecefield

2017-12-29 Thread Justin Lemkul 



On 12/29/17 7:43 AM, Dilip H N wrote:

Hello all,
How to find out/search a specific molecule or ion is present in which
forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
molecule), and hence can generate .pdb file corresponding to that residue
naming in the FF and generate its topology.

In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
which forcefield is it present.

Any suggestions...


Both are in CHARMM36. Ca2+ is CAL and carbonate is CO3.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Regarding finding a ion/molecule in forecefield

2017-12-29 Thread Dilip H N 
Hello all,
How to find out/search a specific molecule or ion is present in which
forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
molecule), and hence can generate .pdb file corresponding to that residue
naming in the FF and generate its topology.

In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
which forcefield is it present.

Any suggestions...

Thank you.


-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



 Sent with Mailtrack

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