[gmx-users] Re: hi Gromacs error

[Justin A. Lemkul]

Please add the attached file to the gromos43a1p.ff directory.

-Justin

kalai arasan wrote:
> justin,
>         I am sorry to disturb you again, i just like to convey the 
> information i got another error while using version 4.5.3 
> 
> 
> ---------------------------------------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3 
> Source code file: resall.c, line: 581
> 
> Fatal error:
> Residue 'HISE' not found in residue topology database
> ---------------------------------------------------------------------------------------
> 
> I searched in many links but i am not able to solve it.
> 
> On Fri, Jul 29, 2011 at 12:34 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
>     I believe this was a bug in Gromacs that was fixed many years ago.
>      Version 3.3 is antiquated and severely outdated.  I would advise
>     you to upgrade to version 4.5.4 and try again with the attached
>     files, which have been reformatted to be compatible with the newer
>     version.  Beyond this, I cannot suggest any other remedy.
> 
>     -Justin
> 
>     kalai arasan wrote:
> 
>         Justin,
> 
>                   Thank you for the files, but still i am facing
>         problem. Now it showing
>         ------------------------------__------------------------------__-----------------------------
>         Program pdb2gmx, VERSION 3.3
>         Source code file: resall.c, line: 331
> 
>         Fatal error:
>         in .rtp file at line:
> 
>         ------------------------------__------------------------------__------------------------------__-
>         Please help me out to solve the problem.
>         with regards
>         kalai
> 
>         On Wed, Jul 27, 2011 at 4:49 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
>            The files are attached.  Please read the README carefully.
> 
>            -Justin
> 
> 
>            kalai arasan wrote:
> 
>                Justin,
>                I am kalai from India, working in gromacs.
>              
>          http://oldwww.gromacs.org/____pipermail/gmx-users/2008-____January/031964.html
>         <http://oldwww.gromacs.org/__pipermail/gmx-users/2008-__January/031964.html>
>              
>          <http://oldwww.gromacs.org/__pipermail/gmx-users/2008-__January/031964.html
>         <http://oldwww.gromacs.org/pipermail/gmx-users/2008-January/031964.html>>
>                I am facing the error while running pdb2gmx command, i
>         saw from
>                above link that you can solve this problem, please help
>         me out.
>                Below i mention the error.
> 
>              
>          ------------------------------____----------------------------__--__--------------------------
>                Program pdb2gmx, VERSION 3.3
>                Source code file: h_db.c, line: 85
> 
>                Fatal error:
>                wrong format in input file ffG43a1p.hdb on line
>                            2         7          OW
>              
>          ------------------------------____----------------------------__--__--------------------------__----__--
> 
>                --         P.Kalaiarasan
>                National Centre of Applied Human Genetics
>                School of Life Sciences
>                JNU
>                New Delhi
>                India
> 
> 
>            --     ==============================____==========
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
> 
>            ==============================____==========
> 
> 
> 
> 
>         -- 
>         P.Kalaiarasan
>         National Centre of Applied Human Genetics
>         School of Life Sciences
>         JNU
>         New Delhi
>         India
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
> 
> 
> 
> 
> -- 
> P.Kalaiarasan
> National Centre of Applied Human Genetics
> School of Life Sciences
> JNU
> New Delhi
> India
> 

-- 
========================================

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

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