Dear Amber Users,
I have run MD on my protein for 12ns. I was able to combine all the MD trajectories into one .binpos file. When I try to image the protein using ptraj, I run into problems. The output .mdcrd does not load well in VMD. The atoms seem to be streaking all over the box. The ptraj script I used is given below: ANy help to resolve this problem is greatly appreciated. Thanks.
Jaya.
trajin ../2ns_md/2a6_md2.mdcrd 1 500 25
trajin ../2ns_md/2a6_md3.mdcrd 1 500 25
trajin ../2ns_md/2a6_md4.mdcrd 1 500 25
trajin ../2ns_md/2a6_md5.mdcrd 1 500 25
trajin ../2ns_md/2a6_md6.mdcrd 1 500 25
trajin ../2ns_md/2a6_md7.mdcrd
trajin ../2ns_md/2a6_md8.mdcrd
trajin ../2ns_md/2a6_md9.mdcrd
trajin ../2ns_md/2a6_md10.mdcrd
trajin ../2ns_md/2a6_md11.mdcrd
trajin ../2ns_md/2a6_md12.mdcrd
trajin ../2ns_md/2a6_md13.mdcrd
trajin ../2ns_md/2a6_md14.mdcrd
trajin ../2ns_md/2a6_md15.mdcrd
trajin ../10ns_md_ht/2a6_md18.mdcrd
trajin ../10ns_md_ht/2a6_md19.mdcrd
trajin ../10ns_md_ht/2a6_md20.mdcrd
trajin ../10ns_md_ht/2a6_md21.mdcrd
trajin ../10ns_md_ht/2a6_md22.mdcrd
trajin ../10ns_md_ht/2a6_md23.mdcrd
trajin ../10ns_md_ht/2a6_md24.mdcrd
trajin ../10ns_md_ht/2a6_md25.mdcrd
trajin ../10ns_md_ht/2a6_md26.mdcrd
trajin ../10ns_md_ht/2a6_md27.mdcrd
trajin ../10ns_md_ht/2a6_md28.mdcrd
trajin ../10ns_md_ht/2a6_md29.mdcrd
trajin ../10ns_md_ht/2a6_md30.mdcrd
trajin ../10ns_md_ht/2a6_md31.mdcrd
trajin ../10ns_md_ht/2a6_md32.mdcrd
trajin ../10ns_md_ht/2a6_md33.mdcrd
trajout 2a6_md_2_33.mdcrd nobox
center :1-465 mass origin
image origin center
rms first mass out rms_to_first.data :1-465
average avg.pdb :1-465 pdb
strip :WAT
go
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Received on Wed May 12 2010 - 11:30:06 PDT
