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

[Ozbil, Mehmet]

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.

 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
    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

==================================================
--
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-request at gromacs.org.