AMBER Archive (2004)

Subject: Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd

From: Anna Schrey (
Date: Fri Jan 23 2004 - 04:39:47 CST

Dear Kristina and David,

thank you for your hints. Setting the eedmeth parameter to 5 was indeed
very helpful (the Amber 7 calculations performed moe similar to the
Amber 5 calculation). Unfortunately, settig the cutoff to 999 did noch
improve the minimization.
However, the final solution was 1. to constrain the CA by harmonic
restraints and 2. to set nsnb from 25 to 10. According to further
experience in our group, nsnb=10 seems to be a good value for vacuum
minimizations using AMBER7.

best regards,


Kristina Furse wrote:
> Anna-
> Don't quote me on this ;-) and hopefully someone with more experience will
> chime in, but it is my understanding that amber7 has been optimized for
> solvent calculations, while older versions, like amber5 are more for vacuum
> calc's. Since you have ntb=0, for your infile, I'm assuming you're doing
> vacuum. For your amber7 runs, you should add an &ewald section and set the
> flag eedmeth=5 to get an appropriate vacuum calc in amber7. (see older posts
> on eedmeth--it's not an ewald flag even though it's in the &ewald section...).
> When I want to do vacuum calcs, I typically just use sander_classic--it does
> vacuum like amber5 did.
> Good luck!
> Kristina
>>===== Original Message From Anna Schrey <> =====
>>dear AMBER community,
>>I am trying to minimize a protein containing a - manually parametrized -
>>small-molecule ligand. This is my sander input file
>> &cntrl
>> imin=1, scee=1.2,
>> ntpr=100, maxcyc=10000,
>> cut=8.0,
>> dielc=1,
>> nsnb=25, ntr=0, drms=x,
>> ntmin=0, ncyc=10, ntb=0,nmropt=y,
>> &end
>> &wt type='END' &end
>>LISTOUT= MINRUNamb51_0_nsmb100_4.violations
>>Positional restraints on TM domains
>>CA * * *
>>RES 1 319
>>I setup a followup of minimizations with different drms limits (1, 0.5,
>>0.1, 0.05, 0.01) and calculated with nmropt both 0 and 1 (the results
>>were similar). Using AMBER 5, I got down to rmsd about 0.1. Using AMBER
>>7, I only got down down to about 0.5, including several LINMIN FAILUREs.
>>Setting the nsnb value to 100 had no effect.
>>I would be pleased if somebody would be able to help me.
>>Best regards,
>>The AMBER Mail Reflector
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> ****************************************************
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> email:

Dr. Anna K. Schrey
Forschungsinstitut fuer Molekulare Pharmakologie   Phone: +49-30-94793-231
Robert-Roessle-Strasse 10                          Fax:   +49-30-94793-169
D-13125 Berlin, Germany                            email:

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