HELP with Water generation

Anurag Joshi joshi at iastate.edu
Thu Sep 21 14:10:38 EST 1995


hi everyone

i am trying to generate a box of watr molecules as described in the
manual. I am having difficulties and would be greatly obliged if someone
could help me out with this

the prg as written in the book is
=================== 
segment 
    
      name="WAT"
      chain 
	  molecule TIP3  number=125 end
 end

 end
======================================
i wrote this program
========
remark file generate.inp
remark generate structure file for 125 water molecules

 topology  @toppar/toph19.sol

 end

 parameters
 
 @toppar/param19.sol




 {  nbonds                                  {*This statement specifies the  *}
      atom cdie shift eps=1.0  e14fac=0.4  {*nonbonded interaction energy  *}
      cutnb=7.5 ctonnb=6.0 ctofnb=6.5      {*options.  Note the reduced    *}
      nbxmod=5 vswitch                     {*nonbonding cutoff to save some*}
   end                                     {*CPU time.   This statement    *}
                                           {*overwrites the defaults in    *}
                                           {*the parameter file.           *}

}
 end
 segment 
    
      name="WAT"
      chain  end
        molecule name = TIP3  number=125 end
 end

 end

 write coordinates output= water.pdb end

 write structure output= water.psf   end

stop
==================

now i do generate a pdb file but all the atoms ahave the same coordinate.
i dont know how that is happening,also the coordinate is the maximum
possible.
this is a part of my pdb file
======================
REMARK FILENAME="water.pdb"
REMARK   PARAM19.SOL (water parameters)
REMARK   ===========
REMARK   available: TIPS3P model
REMARK DATE:13-Sep-95  15:39:20       created by user: joshi
ATOM      1  OH2 TIP3    1    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      2  H1  TIP3    1    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      3  H2  TIP3    1    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      4  OH2 TIP3    2    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      5  H1  TIP3    2    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      6  H2  TIP3    2    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      7  OH2 TIP3    3    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      8  H1  TIP3    3    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM      9  H2  TIP3    3    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     10  OH2 TIP3    4    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     11  H1  TIP3    4    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     12  H2  TIP3    4    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     13  OH2 TIP3    5    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     14  H1  TIP3    5    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     15  H2  TIP3    5    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     16  OH2 TIP3    6    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     17  H1  TIP3    6    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     18  H2  TIP3    6    9999.0009999.0009999.000  1.00  0.00      WAT 
ATOM     19  OH2 TIP3    7    9999.0009999.0009999.000  1.00  0.00      WAT 
========================
my log file is as follows
==========
 X-PLOR: V3.1f user: joshi        on: sgi             at: 13-Sep-95 15:39:20

 Author: Axel T. Brunger
 Copyright: 1988-92 (Yale University), 1987 (Harvard University)

 X-PLOR>remark file generate.inp 
 X-PLOR>remark generate structure file for 125 water molecules 
 X-PLOR> 
 X-PLOR> topology  @toppar/toph19.sol 
 ASSFIL: file toppar/toph19.sol opened.
 RTFRDR>remarks  TOPH19.SOL 
 RTFRDR>remarks  ========== 
 RTFRDR>remarks  topology file for solvent molecules 
 RTFRDR>remarks  water models available: TIP3P model 
 RTFRDR> 
 RTFRDR>set echo=false end 
 RTFRDR> 
 RTFRDR> end 
 X-PLOR> 
 X-PLOR> parameters 
 PARRDR> 
 PARRDR> @toppar/param19.sol 
 ASSFIL: file toppar/param19.sol opened.
 PARRDR>remarks   PARAM19.SOL (water parameters) 
 PARRDR>remarks   =========== 
 PARRDR>remarks   available: TIPS3P model 
 PARRDR> 
 PARRDR>set echo=false end 
 PARRDR> 
 PARRDR> 
 PARRDR> 
 PARRDR> 
 PARRDR> {  nbonds                                  {*This statement specifies the  *} 
 PARRDR>      atom cdie shift eps=1.0  e14fac=0.4  {*nonbonded interaction energy  *} 
 PARRDR>      cutnb=7.5 ctonnb=6.0 ctofnb=6.5      {*options.  Note the reduced    *} 
 PARRDR>      nbxmod=5 vswitch                     {*nonbonding cutoff to save some*} 
 PARRDR>   end                                     {*CPU time.   This statement    *} 
 PARRDR>                                           {*overwrites the defaults in    *} 
 PARRDR>                                           {*the parameter file.           *} 
 PARRDR> 
 PARRDR>} 
 PARRDR> end 
 X-PLOR> segment 
 SEGMENT> 
 SEGMENT>      name="WAT" 
 SEGMENT>      chain  end 
 SEGMENT>        molecule name = TIP3  number=125 end 
 SEGMENT> end 
 SEGMNT:   125 residues were inserted into segment "WAT "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=        375(MAXA=       16000)  NBOND=        250(MAXB=       16000)
 NTHETA=       125(MAXT=       24000)  NGRP=         125(MAXGRP=     16000)
 NPHI=           0(MAXP=       30000)  NIMPHI=         0(MAXIMP=      8000)  
 NDON=           0(MAXPAD=      4000)  NACC=           0(MAXPAD=      4000)
 NNB=            0(MAXNB=       3000) 
 X-PLOR> 
 X-PLOR> end 
 %X-PLOR-ERR: "END" not allowed. "STOP" terminates program
 X-PLOR> 
 X-PLOR> write coordinates output= water.pdb end 
 ASSFIL: file water.pdb opened.
 X-PLOR> 
 X-PLOR> write structure output= water.psf   end 
 ASSFIL: file water.psf opened.
 X-PLOR> 
 X-PLOR>stop 
 CSTACK: size=    40000 used=      150 current=        0
 HEAP:   maximum use=    30008 current use=        0
 X-PLOR: total CPU time=      0.2800 s
 X-PLOR: entry time at 15:39:20 13-Sep-95
 X-PLOR: exit time at 15:39:21 13-Sep-95

=======================

I will really appreciate if someone could help me out with this as i am
a beginer with Xplor.


thanks a lot for your patience and help

anurag joshi
dept of chemical eng ,
Iowa State Univ.
Ames
USA

-- 
anurag joshi
joshi at iastate.edu




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