AMBER Archive (2009)

Subject: RE: [AMBER] problem in input

From: Rausch, Felix (frausch_at_ipb-halle.de)
Date: Fri Apr 03 2009 - 03:04:36 CDT


Hello.

I'm not sure about that, but is it possible that you forgot to declare your
reference-file in the command line call within the "-rest"-flag?
Furthermore, you have to recheck all the parameters in the input file because
of switching from a periodic to a non-periodic run.

In any case, it would be very helpful to see more of your output (maybe
everything until the error occured).

Kind Regards,
Felix Rausch

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of balaji nagarajan
Sent: Thu 4/2/2009 10:23 PM
To: amber forumnew
Cc:
Subject: RE: [AMBER] problem in input

dear amber
i changed ntb = 0
now its giving the error as

   5. REFERENCE ATOM COORDINATES

| INFO: Old style inpcrd file read

FATALEFERENCE ATOM COORDINATES

what is the mistake
could any one help me out to solve this
regards
balaji
UOM

                        

> Subject: RE: [AMBER] problem in input
> Date: Thu, 2 Apr 2009 13:08:27 +0200
> From: frausch_at_ipb-halle.de
> To: amber_at_ambermd.org
>
> Hello.
>
> Like mentioned in the manual p.53 , the Generalized Born models are only
> available for non-periodic calculations, i.e. where ntb = 0.
>
> Regards,
> Felix Rausch
>
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org on behalf of balaji nagarajan
> Sent: Thu 4/2/2009 12:29 PM
> To: amber forumnew
> Cc:
> Subject: [AMBER] problem in input
>
> dear Amber !
>
> I am doing targeted molecular dynamics ,
> with explicit solvent , I have used the following script as input
>
>
> &cntrl
> imin = 0,
> irest = 1 ,
> ntb =2,
> pres0 = 1.0,
> ntp = 1,
> ntxo = 1,
> ntx =7,
> tempi =300.0,
> ntc=3,
> ntr =0,
> ntf = 2,
> igb = 1,
> nscm = 100,
> ntwr = 100
> ntpr = 100,
> ntwx = 100,
> ntwv =100,
> ntwe = 100,
> nsnb = 20,
> offset = 0.13,
> ntt = 3,
> gamma_ln = 3.0,
> temp0 = 300.0
> nstlim = 2000000,
> dt = 0.001,
> cut = 12.0,
> itgtmd=1,
> tgtrmsd =0 ,
> tgtmdfrc =0.01,
> tgtfitmask= ":1- 76"
> tgtrmsmask= ":1- 76"
>
> when i run this it gives the error as follows !
>
>
>
>
>
> (NTB /= 0 && NTP /= 0) but IFBOX == 0
> This combination is not supported
>
> BOX is too small: 0.000 0.000 0.000
>
> igb>0 is only compatible with ntb=0
>
> *** input error(s)
>
> could any one suggest me where i have done mistake
> thank you in advance
>
> balaji
> UOM
>
>
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