To generate the topology and crd file I used these commands for
protein,complex and drug
tleap
source leaprc.gaff
loadamberprep drug.prepin
loadamberparams drug.frcmod
var=loadpdb complex.pdb
saveamberparm var complex.top complex.crd
addions var Na+ 0
solvatebox var TIP3PBOX 8.0
solvateoct var TIP3PBOX 8.0
saveamberparm var complex_wat.top complex._wat.crd
quit
Last three columns of Final lines in the crd file are same as you said but
initial three columns are not .It reads like this.
122.7835660 124.3828400 147.1166520 90.0000000 90.0000000 90.0000000
What shall I do?I did it repeatedly but the same problem persist.Please
help.
Thanks
Regards
Ashutosh Shandilya
On 3 May 2010 19:38, case <case.biomaps.rutgers.edu> wrote:
> On Sun, May 02, 2010, ashutosh shandilya wrote:
> >
> > *I encounter this problem when I run sander for water *
> > * relaxation, *
> > * *
> > * Error: ifbox=2 in prmtop but angles are not correct *
>
> How did you create the prmtop and input coordinate files? When ifbox=2 in
> the
> prmtop file, the final line of the input coordinate file should look like
> this:
>
> 56.5123496 56.5123496 56.5123496 109.4712190 109.4712190 109.4712190
>
> The first three numbers should be the same, but will not be 56.5 for other
> systems. The final three numbers (the unit cell angles) should be 109.47.
>
> The program is finding angles is doesn't expect, but has no way to know
> (nor
> do we) how this came about.
>
> ...dac
>
>
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Received on Tue May 04 2010 - 04:00:04 PDT
