AMBER Archive (2003)

Subject: nmanal & quasih question

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Wed Jan 08 2003 - 01:16:56 CST

Greetings all,
  I try to do nmanal analysis for my peptide which contains 180 atoms
after calculating normal modes via nmode & quasih, but nmanal returns
lots of error messages as follows, (I run AMBER7 on IBM P690) 

--
A READ statement using decimal base input found the invalid digit '?' in
the input file.  The program will recover by assuming a zero in its place.

(ps:'?' represent as follows,)

% F L A G T I T L E % F O R M A T ( a ) . E
+ . E - . E - . E - . . E - . E - . E + . E - . . E + . E + . E + . E + .
. E + - . E + . E + . E + . . E + - . E + . E - . E - . . E - . E - . E -
. E - . . E - - . E - . E + . E + - . . E + . E + - . E + . E + - . . E -
. E - . E - . E - . . E - . E + . E + . E - . . E + - . E + . E + . E + .
. E + - . E + - . E + . E - . . E - . E - . E - . E - - . . E - . E - - .
(......to be omitted)
 + . E + . . E + . E + . E + . E + . % F L A G B O ND S _ I N C _ H Y D R
 O G E N % F O R M A T ( I ) % F L A G B O N D S _ W I T H O U T _ H Y D R
O G E N % F O R M A T ( I ) % F L A G A N G L E S _ I N C _ H Y D R O G E
N % F O R M A T ( I ) % F L A G A N G L E S _ W I T H O U T _ H Y D R O G
E N % F O R M A T ( I ) % F L A G D I H E D R A L S _ I N C _ H Y D R O G
E N % F O R M A T ( I ) % F L A G D I H E D R A L S _ W I T H O U T _ H Y
D R O G E N % F O R M A T ( I ) I N F I N F I N F I N F I N F I N F I N F
......

I doubt if nmanal read in prmtop7 with some problems, because the same
prmtop7 can be read in well by nmode. I also try to convert prmtop7 to old
prmtop, but nmanal still fails when read in old prmtop.
--
nmanal -O -i nmdin -o nmdout -p 11pep.nmode.top -v quasih.vecs

nmdin:
---------------------
nmanal for 11pep

 &data
     ntrun=1,
     nvect=50,
     ibeg=1,
     iend=50,
     ivform=1,
     natom=180,
     ihsful=1,
 &end
---------------------

I also check quasih.vecs after running quasih without error messages,
there are some 'INF' string appears in quasih.vecs which should
originally be a number. I've no idea what happens to it.
--
quasih < 2ns.nowat.trj -natom 180 -f 2 -m mass -x xyz -v quasih.vecs
-first 5300 -last 6300 -nmode 50

( 'nmode' was produced by NMODE)

Thanks for any help and ideas.

Best Regards,

sychen.