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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Received on Tue Jul 12 2005 - 14:53:01 PDT
