Hello
Sorry, I don't mean to inundate the web site, but I need help if possible. I finally got AMBER11 and AmberTools1.4 compiled (serially) but, I am having problem in their performance. I have been using AMBER8 in the past, but have just started using AMBER11.
AMBER11 problem:
I serially compiled AMBER11 and it did pass all its tests. However, when I do a MD run Sander does start the run and finish with a complete output file that shows no problem. I have, in the command line, tagged to save a restart file and a mdcrd file. It does save a restart file, but it DOES NOT save a mdcrd file. That is, my file "test.mdcrd" is empty although it writes the file's name and places it in my directory.
AmberTools1.4 problem:
I have serially compiled AmberTools1.4 (with all bugfixes) and ran the tests without any errors. However, when I run ptraj to combine multiple trajectories and then run "rdparm" to "checkcoords" get the following error:
RDPARM MENU: checkcoords RNAP_openMD34_35.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: RNAP_openMD34_35.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 230188 FrameSize: 5593594 TitleSize: 30 NumBox: 3 Seekable 0
File (RNAP_openMD34_35.mdcrd) is an AMBER trajectory with box coordinates
If I use a single trajectory file (i.e. one from a MD run) to obtain the RMS there is no problem. It is only when I COMBINE the trajectory files.
I am using AMBER8 trajectories and a prmtop file from AMBER8..Should this make a difference??
Can someone please give me some adivce.
Thanks Steve
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Received on Thu Jun 24 2010 - 10:30:08 PDT
