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.war...@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.war...@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-boun...@gromacs.org
>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
>> Sent: Thursday, 30 April 2009 9:07 AM
>> To: jalem...@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
>> <jalem...@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
>> >
>> > ========================================
>> > _______________________________________________
>> > gmx-users mailing list gmx-us...@gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search
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>> >
>>
>>
>>
>> --
>> Yanmei Song
>> Department of Chemical Engineering
>> ASU
>> _______________________________________________
>> gmx-users mailing list gmx-us...@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
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> _______________________________________________
> gmx-users mailing list gmx-us...@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
Yanmei Song
Department of Chemical Engineering
ASU
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