AMBER Archive (2006)

Subject: AMBER: distance dependent dielectric constant

From: Mahalakshmi Sahasranaman (mlakshmis_at_gmail.com)
Date: Wed May 17 2006 - 05:36:55 CDT

Dear Amber users,

 I want to do a energy minimization in vacuo using a distance-dependent
dielectric constant to mimic bulk solvent effects.
When I run Sander for doing energy minimization, it gives me the following
error message :

$AMBERHOME/exe/sander -O -i dna_vac_min.in -o dna_vac_min.out -c
dna_charges_cio.inpcrd -p dna_charges_cio.prmtop -r a-dna_vac_min.rst
forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
5, file /home/nmr/lakshmi/anwer/dna_vac_min.in, line 10, position 8
Image PC Routine Line Source
sander 0819B312 Unknown Unknown Unknown
sander 081999E5 Unknown Unknown Unknown
sander 0817AE7D Unknown Unknown Unknown
sander 0814572A Unknown Unknown Unknown
sander 0814545A Unknown Unknown Unknown
sander 0815D198 Unknown Unknown Unknown
sander 080A8E8A Unknown Unknown Unknown
sander 08074878 Unknown Unknown Unknown
sander 0807458A Unknown Unknown Unknown
sander 0804A365 Unknown Unknown Unknown
libc.so.6 003E6E33 Unknown Unknown Unknown
sander 0804A2A1 Unknown Unknown Unknown

My input file for Sander is given below :

dna in vacuo
&cntrl
 imin=1,
 maxcyc=700,
 ncyc=200,
 ntb=0,
 igb=0,
 cut=12,
 dielc=1,
 eedmeth=5
/

Could you please tell me how to do a energy minimization in vacuum using
distance dependent dielectric constant ? What are the parameters to be
included to do this ?

Thanks,
Lakshmi

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