AMBER Archive (2006)

Subject: AMBER: Amber 9 installation problem

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Oct 19 2006 - 10:43:02 CDT

Dear Amber community,
 I have installed Amber9 for the first time using ifortx86_64 and intel's mkl library on PC-Linux SUSE 10.0. After the installation, execution of sander gave me the following error message:
 
 sander: error while loading shared libraries: libvml.so: cannot open shared object file: No such file or directory
 
 Could someone please let me know how to troubleshoot this libvml.so problem.
 
 best regards,
 
 jenk.

 
 
 Thomas Cheatham <tec3_at_utah.edu> wrote:
> What I would like to know is whether or not the following ptraj input
> command is OK to determine the phase angles of ribose sugar residue 1
> taking the dihedral angle about C2'-C3' as the bases and the O4' atom as
> the fifth atom to constitute a pseudorotational angle.
>
> Here is my ptraj input :
>
> traj.in dna.binpos
> pucker res1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out phaseangle.out time 0.2

Yes, this is what I routinely do...

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