Re: [AMBER] Amber

From: Jason Swails <>
Date: Thu, 24 Mar 2011 08:21:56 -0700


2011/3/23 Ц <>

> Hello,
> I have two questions to consult.
> Firstly, I want to do the molecular dynamic simulation between RNA and its
> ligand, so I uploaded the complex of the RNA and the ligand. Using
> leaprc.ff03 force field, there is no corresponding parameters for U. How can
> I do? Choose another force filed, such as leaprc.rna.ff02?

The problem here is actually the PDB standard, I believe. ff03 loads the
all_nucleic94.lib nucleic acid residue template, which follows the old
standard. That standard used R for RNA residue names (i.e. RU, RA, RG, RC),
whereas the new standard simply uses the letter (i.e. U, A, G, C). Newer
force fields (i.e. ff03.r1) have conformed to this change, but leaprc.ff03
offers no support here. My suggestion is to use a more recent force field
(such as ff99bsc0 for ff03.r1, but my strongest suggestion is for ff99bsc0,
which is actually several years newer than ff03).

 Secondly, I do the minimization of some complexes. Some of them have
> abnormal termination without errors at the bottom of the output file. The
> following are the input file and the part of output file. How can I handle
> this problem?
> Thank you very much!

Are you running sander.MPI? pmemd.MPI? Or just the serial version? Look
for error messages printed to stdout by slave threads or error messages
printed to stderr. What seems strange about the chunk of output file you
sent is that the gradient is becoming very very large within 100 steps. The
output file indicates the offending atom (in this case, O4, #2294). Try
printing out restart files every couple steps, and visualize what's
happening with those specific atoms after the minimization fails.

One other suggestion -- since you're most likely using a rigid water model,
perhaps you should consider turning SHAKE on (ntc=2, ntf=2).

Hope this helps,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Mar 24 2011 - 08:30:05 PDT
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