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
first.
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.
-Justin
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" <[email protected]>
Subject: RE: [gmx-users] [gmx-user]Error by pdb2gmx
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
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
[email protected]
+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
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
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