[gmx-users] Error by pdb2gmx

[Yanmei Song]

Hi, Dallas:

I added this to the ffoplsaa.rtp

[ PDM ]

[ atoms ]
      SI       SI                 0.300     1
   CH3      opls_069    0.000     1
       O       opls_108   -0.300     1

 [ bonds ]
    SI     O
    SI   CH3


 [ dihedrals ]
   CH3    SI    O      SI     dih_PDM_chi1_C_SI_O_SI
      SI     O   SI   CH3     dih_PDM_chi1_SI_O_SI_C
       O    SI    O      SI      dih_PDM_chi1_O_SI_O_SI

The format is the same with other entries. Do you guys think anything
wrong with it?

Also what does it mean by the error message:

Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms

 chain  #res #atoms
 1 'A'     1     45

All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289

Fatal error:
in .rtp file at line:


-------------------------------------------------------

what is "Source code file: resall.c, line: 289"  It seems the problem
comes from here.

Thanks a lot!


On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
<Dallas.Warren at pharm.monash.edu.au> wrote:
> Check consistency with other entries around it, easy way to check to see that you have the right format.
>
> What did you edit the file with?
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology and Pharmacology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org
>> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
>> Sent: Thursday, 30 April 2009 9:07 AM
>> To: jalemkul at vt.edu; Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Error by pdb2gmx
>>
>> This is the new entry I added to the rtp file.
>>
>> [ PDM ]
>>
>>
>>  [ atoms ]
>>     SI      SI              0.300     1
>>    CH3    opls_069    0.000     1
>>      O      opls_108   -0.300     1
>>
>>
>>  [ bonds ]
>>     SI     O       0.190    158805.0
>>     SI   CH3     0.164    293160.0
>>
>>
>>  [ dihedrals ]
>>    CH3    SI    O    SI   3.77    3     0
>>     SI     O   SI   CH3   3.77    3     0
>>      O    SI    O    SI     3.77    3     0
>>
>>
>> On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
>> <jalemkul at vt.edu> wrote:
>> >
>> >
>> > Yanmei Song wrote:
>> >
>> >> -------------------------------------------------------
>> >> Program pdb2gmx, VERSION 3.3.3
>> >> Source code file: resall.c, line: 289
>> >>
>> >> Fatal error:
>> >> in .rtp file at line:
>> >>
>> >>
>> >> -------------------------------------------------------
>> >
>> > Well that's not a terribly helpful error message, is it? :)
>> >
>> > There is probably something wrong with the .rtp entry you
>> created.  If you
>> > can post that, perhaps someone can spot it.
>> >
>> > -Justin
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Ph.D. Candidate
>> > ICTAS Doctoral Scholar
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > _______________________________________________
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>>
>>
>>
>> --
>> Yanmei Song
>> Department of Chemical Engineering
>> ASU
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-- 
Yanmei Song
Department of Chemical Engineering
ASU