AMBER Archive (2009)

Subject: RE: [AMBER] help- regarding - TMD

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (shaowen.hu-1_at_nasa.gov)
Date: Thu Apr 16 2009 - 08:30:22 CDT

Could you please post more information like the script you run the code? And how you prepared the target and initial systems? Hope somebody who have done similar work can help you. I am still doing tests with implicit solvent.

Best,
Shaowen

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan
Sent: Thursday, April 16, 2009 12:21 AM
To: amber forumnew
Subject: RE: [AMBER] help- regarding - TMD

Dear AMBER ,
thank you Shaowen!

I have given this at the end of my script , but still
i have the same problem
sander.MPI is running and the out put is not printed

i dont know how to slove this
regards
balalji
UOM

> From: shaowen.hu-1_at_nasa.gov
> To: amber_at_ambermd.org
> Date: Wed, 15 Apr 2009 12:56:07 -0500
> Subject: RE: [AMBER] help- regarding - TMD
>
> You may try to add
>
> tgtrmsd = xx.xxxx
> /
> &wt
> TYPE='TGTRMSD', istep1=1, istep2=2000000,
> value1 = xx.xxxxx, value2 = 0.0,
> /
> &wt
> type="END",
> /
>
> to the end of your input file, where xx.xxxx is the rmsd of your initial "1-76" from the target.
>
> Best,
> Shaowen
>
> ________________________________________
> From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu_at_hotmail.com]
> Sent: Wednesday, April 15, 2009 10:19 AM
> To: amber forumnew
> Subject: [AMBER] help- regarding - TMD
>
> Dear Amber ,
>
> I am giving targeted molecular dynamics with explicit water
>
> when i gave the following script
> sander.MPI is running .
> but when i see the out put file
> tail -f tmdscript.out
> its not printing any thing
> I could not find our the error
>
> help me out to solve this
>
> the script as below
> &cntrl
> imin = 0,
> irest = 0 ,
> ntb = 2,
> ntxo = 1,
> ntx =1,
> tempi =300.0,
> ntc=2,
> ntr =0,
> ntf = 2,
> nscm = 100,
> ntwr = 100
> ntpr = 100,
> ntwx = 100,
> ntwv =100,
> ntwe = 100,
> ntt = 3,
> gamma_ln = 1.0,
> temp0 = 300.0
> nstlim = 2000000,
> dt = 0.002,
> cut = 10.0,
> itgtmd=1,
> tgtrmsd =0 ,
> tgtmdfrc =0.01,
> tgtfitmask= ":1- 76"
> tgtrmsmask= ":1- 76"
>
>
>
>
>
> /
> regards
> balaji
> UOM
>
>
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