AMBER Archive (2005)

Subject: Re: AMBER: Question about Prep file

From: Marc Baaden (baaden_at_smplinux.de)
Date: Fri Jul 22 2005 - 01:38:42 CDT

Dear Armin,

the parameters, prepfiles etc. for the lanthanides (and related calixarene ones)
were used with an older Amber version (v4.1). I just checked, and they still do
work with my older amber executables, but require the prep-link-edit-parm
sequence that was used at the time.

Unfortunately I am not certain about how you would need to go about converting
them to the current Amber 8 format, or whether there are some specific options
for backwards-compatibility built into Leap.

But in any case I think you brought up an interesting question: what should
one do to keep previous work still usable with current amber versions ? Are
there any guidelines about how to convert not only topologies but also input
files. Maybe some of the Amber developers could give us some precious hints ?

Thanks in advance,
Marc Baaden

>>> opitz_at_che.udel.edu said:
>> Amber Community,
>>
>> I downloaded the lanthanide parameters from the AMBER parameter webpage (ht
     tp://pharmacy.man.ac.uk/amber/) lanthanides, Eu(3+), La(3+), Yb(3+) PREP
      FRCMOD Baaden. After unzipping the prep files, I tried to load the Eu3+
     file into leap it stopped with the message "Unexpected EOF: discarding res
     idue ( -50 -50)".Why is this? Is this prep format an older format? How w
     ould I have to
>> modify the file to get it to work?
>> I have pasted the body of the file below as well.
>>
>> Best Regards,
>>
>> Armin
>>
>>
>> M XYZ 1 1 1 1 2 1
>> E EU Eu
>> -50 -50
>> -50 -50 -50
>> -50 -50 -50 -50
>> 1
>> 0
>> 0 1 2 0
>> 1
>> 0
>> 3.0000
>> -0.03100 -0.20000 0.22700
>>
>>
>>
>>
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>>

Marc Baaden 

-- 
 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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