AMBER Archive (2005)

Subject: Re: AMBER: Question about "nmanal"

From: Yen-Ting Lai (c54881028_at_mail.bio.ncku.edu.tw)
Date: Tue Jul 12 2005 - 08:36:25 CDT

I have tried nmanal with ntrun=8, but only get an error message: bad magic
number "rdpa"

The output file(nmdout) contains some lines as:
########################### START of nmdout ##############################
nmr00 169% more nmdout

          ******************************************************
          INITIATE THE NMANAL MODULE OF PROGRAM AMBER
          ******************************************************

No belly:1435 atoms in moving group
 &DATA NTRUN = 8, NVECT = 10, PCUT = 1.99999995529651642E-2, IBELLY = 0,
NTX = 1, IBEG = 1, IEND = 2, NRGRP = 0, IRMS =
 0, NRVEC = 0
  NRAT = 0, IAT = 1, JAT = 1435, IMOV = 0, IFLUC = 0, IPRO = 1, KFORM = 2,
IEFF = 0, BOSE = F, IVFORM = 1, NATOM = 1435,
 IHSFUL = 1,
  FIRST = 1, LAST = 3000, ISKIP = 1, TMAX = 0.E+0, TINTVL = 1. /
.... Core used = 43061
########################### END of nmdout ################################

The input file was:
 try to project
 &data
  ntrun=8,
  nvect=10,
  ibeg=1, iend=2,
  natom=1435,
  first=1,
  last=3000,
  iskip=1,
 &end

The command that I used was: nmanal -O -i nmdin -o nmdout -v vecs -m mass <
../md5-9_no_WAT_NA_fit.mdcrd
I also tried to give the (old) topology file with "-p prmtop", but the
result is the same.

Can anyone help?

Best
Yen

> Thanks for your kind reply. I will try it out anyway.
>
>>
>> Heaven knows, of course, if ntrun=8 in nmanal actually works. This was
>> all
>> re-written for Amber 8 (see the "projection" command in ptraj).
>>
>
> By the way, do you think that it's worthy updating to Amber8. We have
> Amber7 here in Sweden, but soonly I will return to my home country,
> Taiwan, where we only have Amber6(both versions are patched). I noticed
> that the new version of ptraj has some more features that I am interested
> in. However, the standalone version of ptraj is still not available. This
> is the main reason that we want to upgrade to Amber8. Or should we wait
> for Amber9? Will it be released in the near future?
>
> Best regards,
> Yen
>
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