AMBER Archive (2003)

Subject: AMBER: nmanal's rvec file

From: Qiang Lu (qiangl_at_uci.edu)
Date: Tue Aug 19 2003 - 18:19:27 CDT

Hi amber user,

   From nmode to nmanal, nmanal project the normal mode vibrations to
   internal coordinates. I have the output and vector files from
   nmode, parm file. The input file of nmanal is
   & data
      ntrun = 0
      nvect = 200
   & end
   The nmanal command is
   nmanal [-O] -i nmanal.in -o nmanal.out -p zn.parm6 -v nmode.vec -r nmanal.rvec

   However I cannot get nmanal.rvec. Could anyone tell me if the rvec
   file should exist or not at this case?
   

   The nmanal.out look no problem :

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

   1. M O L E C U L A R T O P O L O G Y F I L E :

                                                                                  
No belly: 40 atoms in moving group
 &DATA
 NTRUN= 0,NVECT= 200,PCUT= 1.99999995529652D-002,IBELLY= 0,NTX= 1,IBEG= 7,IEND=
  50,NRGRP= 0,IRMS= 0,NRVEC= 0,NRAT= 0,IAT= 1,JAT= 40,IMOV= 0,IFLUC= 0,IPRO= 1
 KFORM= 2,IEFF= 0,BOSE= F,IVFORM= 1,NATOM= 40,IHSFUL= 1,FIRST= 1,LAST= 9999
 ISKIP= 1,TMAX= 0.0,TINTVL= 1.00000000000000
 /
.... Core used = 29241
 Found only 120 eigenvectors on vecs file

 NORMAL MODE 7 WITH FREQUENCY = 18.5269

                                                            proj. PE%
 bond ND1 ( 16) - ZN ( 17) -0.00108 0.53272
 bond ZN ( 17) - SG ( 31) 0.00038 0.14759
 bond SG ( 7) - ZN ( 17) -0.00037 0.13350
 bond CB ( 36) - SG ( 39) -0.00013 0.05552
 bond CB ( 12) - HB3 ( 14) -0.00009 0.03677

 NORMAL MODE 8 WITH FREQUENCY = 26.8922
   
........ 

-- 
Best regards,
 Qiang                          mailto:qiangl_at_uci.edu

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