[gmx-users] RE: [gmx-user]Error by pdb2gmx (Dallas

Justin A. Lemkul jalemkul at vt.edu
Fri May 28 15:29:09 CEST 2010

佘安奇 wrote:
> Dear Dallas:
>    Thanks a lot for your reply.
>    But I didn't quite understand "no function types defined in your bonds, angles and dihedrals". Could you give more details? 

I think Dallas might have been thinking of a different file; function types are 
not required in individual .rtp entries, but you do have to have a proper 
[bondedtypes] directive at the top of your .rtp file.  A few other comments:

1. The .rtp entry you posted is for DRG2, which does not correspond to the entry 
that pdb2gmx is complaining about ("DRG") and thus we don't know if you've given 
us the right information.  If you're trying to use the DRG2 entry, pdb2gmx would 
still fail, but for a less cryptic reason (no such residue).

2. It appears from the program suffix that you've attempted to compile the 
entire Gromacs suite in parallel.  There is no reason to do this since only 
mdrun is MPI-aware.  I've seen a few reports of buggy behavior being caused by 
weird compilation, so I'd advise that you start out with a reliable installation 

3. If you're trying to generate a topology for a non-repeating small molecule, 
why both with pdb2gmx at all?  The purpose of pdb2gmx is to build larger 
structures composed of repeating building blocks.  It probably would be the same 
amount of effort to simply write the .itp file by hand as it would be to 
generate this .rtp entry.


> Angel
>> Today's Topics:
>>    1. RE: [gmx-user]Error by pdb2gmx (Dallas
>> B. Warren)
>>    2. Re: Virial and Pressure (Mark
>> Abraham)
>>    3. add missing atom (you zou)
>>    4. Gromacs 3.3.3 segmentation fault on
>> SLES10.2 x86_64    Xeon
>>       architecture - Intel Compilers &
>> Intel MKL
>>       (Juan Alejandro Palomino Benito)
>>    5. Re: Gromacs 3.3.3 segmentation fault
>> on SLES10.2 x86_64    Xeon
>>       architecture - Intel Compilers &
>> Intel MKL (David van der Spoel)
>> ----------------------------------------------------------------------
>> Message: 1
>> Date: Fri, 28 May 2010 12:28:04 +1000
>> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
>> Subject: RE: [gmx-users] [gmx-user]Error by pdb2gmx
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>>     <89907EA1DCFB7548A431C13A270F9DD50ABDC294 at prk-exch-01.vcp.local>
>> Content-Type: text/plain; charset=utf-8
>> You have no function types defined in your bonds, angles
>> and dihedrals.
>> Catch ya,
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of 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. 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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