[gmx-users] Re: hi Gromacs error

[Justin A. Lemkul]

Sorry all, disregard this.  It was intended to be sent to someone else.  Stupid 
email autocompletion...

-Justin

Justin A. Lemkul wrote:
> 
> 
> 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      Version 3.3 is antiquated and severely outdated.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

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