[gmx-users] free energy calculations for reference state for constant pH MD simulations...

[Justin Lemkul]

On 2/10/14, 4:35 PM, Ozbil, Mehmet wrote:
> Yes the error message indicates about the line which is in the very end ( 6  7  2 gb_27). I can see which atoms they are, 6 and 7, but I don`t know how to solve it??? My part of top file is below, with the line it is complaining about in bold. Thank you very much.
>

In this case, it's probably not a significant warning, the reason being that the 
atom types are unchanged.  grompp notices that you're changing the charges, so 
technically the B-state is different, in which case new bonded parameters 
(strictly speaking) are required, because the molecule is different.  In this 
case, the bond wouldn't change, so copying the A-state parameters to the B-state 
is probably fine.  It's a moot point if you are using constraints.

>   Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
> #include "H3O.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
> ; residue  98 GLU rtp GLUH q  0.0
>       1         NL     98    GLU      N      1      -0.66    14.0067   ; qtot -0.66
>       2          H     98    GLU     H1      1       0.44      1.008   ; qtot -0.22
>       3          H     98    GLU     H2      1       0.44      1.008   ; qtot 0.22
>       4        CH1     98    GLU     CA      2      -0.22     13.019   ; qtot 0
>       5        CH2     98    GLU     CB      2          0     14.027   ; qtot 0
>       6        CH2     98    GLU     CG      2          0     14.027   ; qtot 0
>       7          C     98    GLU     CD      3       0.33     12.011   C       0.270126         12.011
>       8          O     98    GLU    OE1      3      -0.45    15.9994   O     -0.634874        15.9994
>       9         OA     98    GLU    OE2      3     -0.288    15.9994   OA     -0.634874        15.9994
>      10          H     98    GLU    HE2      3      0.408      1.008   H      0.000         1.0008

Here's where things don't make sense.  Where are you getting the B-state 
charges?  They're giving you a fractional net charge.  If you're going from GLUH 
-> GLU, then everything is simple; just copy the charges from the .rtp entries. 
  Your numbers are similar, but not identical, to GLU in the B-state.

-Justin

>      11          C     98    GLU      C      4       0.33     12.011   ; qtot 0.33
>      12          O     98    GLU     OT      4      -0.45    15.9994   ; qtot -0.12
>      13         OA     98    GLU      O      4     -0.288    15.9994   ; qtot -0.408
>      14          H     98    GLU     HO      4      0.408      1.008   ; qtot 0
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      1     2     2    gb_2
>      1     3     2    gb_2
>      1     4     2    gb_21
>      4     5     2    gb_27
>      4    11     2    gb_27
>      5     6     2    gb_27
>      6     7     2    gb_27
>
>
> mehmet
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Monday, February 10, 2014 4:22 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
>
> On 2/10/14, 3:57 PM, Mehmet Ozbil wrote:
>> Do you have a suggestion how can I solve it Justin?
>>
>
> The error message tells you exactly what the offending line is for the bonded
> interaction and you can easily check your math with regards to the charge.
> Without seeing the entire topology, I can offer nothing else.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================