Hi,
For some reason I unsubscribed from amber list, then joined again 2 days
ago.
But I am not getting the usual subject-wise message from amber rather a
cumbersome "AMBER Digest, Vol 547, Issue 1" kind of stuff.
I checked in the mail options available, but could not figure out why this
is happening.
Please suggest how to receive "subject-wise" Amber list as earlier.
A small portion of this Digest email is given below.
Thank you.
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AMBER Mailing List Digest
Today's Topics:
1. Re: Job stops due to INFO: Old style inpcrd file read
(Jason Swails)
2. gaff atom type (inhee park)
3. Re: Antechamber atom types and all_nuc94.in atom descriptions
(Kamali Sripathi)
4. problem with tleap (Rejwan)
5. Re: problem with tleap (Jason Swails)
6. Re: Graphene topology from GAFF (Hector A. Baldoni)
7. tleap has error by applying amber ff03ua (Chris Moth)
8. Re: Graphene topology from GAFF (Dan Piraner)
9. Re: problem with tleap (Rejwan)
10. Re: MMPBSA.py and cpptraj error (Sorensen, Jesper)
11. Re: MMPBSA.py and cpptraj error (Sorensen, Jesper)
12. Re: Antechamber atom types and all_nuc94.in atom descriptions
(FyD)
13. Nonbond cells need to be recalculated, restart simulation
from previous checkpoint with a higher value for skinnb. (???)
14. Re: MMPBSA.py and cpptraj error (Jason Swails)
15. Re: Nonbond cells need to be recalculated, restart simulation
from previous checkpoint with a higher value for skinnb.
(Jason Swails)
16. Re: Cellulose NVE with pmemd.cuda.MPI (Ross Walker)
17. Re: tleap has error by applying amber ff03ua (David A Case)
18. Re: Need a higher value for SKINNB (Hailin Huang)
19. Re: A and Z-DNA (Collins Nganou)
20. Re: A and Z-DNA (arnab bhattacharya)
21. Re: A and Z-DNA (Collins Nganou)
22. Re: qmcut in QM/MM simulation with AMBER/GAUSSIAN (Eric Berquist)
23. Re: problem with tleap (Rejwan)
24. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
25. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
26. Thanks (Hunter Brown)
27. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Jonathan Gough)
28. Curious behavior of cpptraj in ambertools 13.1 (Fabr?cio Bracht)
29. Update 10 for AmberTools 13: CPPTRAJ (Daniel Roe)
30. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
31. Re: Cellulose NVE with pmemd.cuda.MPI (Scott Le Grand)
32. Re: Curious behavior of cpptraj in ambertools 13.1 (Daniel Roe)
33. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
34. Re: ERROR: GPU runs fail with nfft Error only when running 2x
geforce TITANS in same machine (Scott Le Grand)
35. Re: Need a higher value for SKINNB (Scott Le Grand)
36. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
37. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
38. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
39. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
40. Re: Curious behavior of cpptraj in ambertools 13.1 (Jason Swails)
41. Re: Need a higher value for SKINNB (Hailin Huang)
42. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Daniel Roe)
43. Experiences with GTX 780 in the framework of Amber
calculations ? (Marek Maly)
44. Re: Update 10 for AmberTools 13: CPPTRAJ (Jan-Philip Gehrcke)
45. Difficulty running sander (Hunter Brown)
46. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Robert Konecny)
47. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
48. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Marek Maly)
49. Re: Protein leaving periodic box (Hailin Huang)
50. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
51. NAB extract residue from molecule (Le,Huy Tuan)
52. Re: Experiences with GTX 780 in the framework of Amber
calculations ? (Gould, Ian R)
53. Re: experiences with EVGA GTX TITAN Superclocked - memtestG80
- UNDERclocking in Linux ? (Scott Le Grand)
54. Re: Experiences with GTX 780 in the framework of Amber
calculations ? (Gould, Ian R)
55. Re: Experiences with GTX 780 in the framework of Amber
calculations ? (Scott Le Grand)
56. Re: Need a higher value for SKINNB (Scott Le Grand)
----------------------------------------------------------------------
Message: 1
Date: Tue, 18 Jun 2013 15:03:29 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Job stops due to INFO: Old style inpcrd file read
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3q8k_-yHgNo=n9_uxAQKWaYW+x=rG9q6LVU-x+gZ1UpBA.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Tue, Jun 18, 2013 at 2:23 PM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Hi Jason,
> Thanks for the quick reply and the suggestion about the cutoff. But I
> would like to bring to your attention that I have a simple protein
> (basically a single protein, not a complex). Although I tried to run the
> simulation with a higher cut-off as you suggested, the error massage is
> again the same that I posted in my previous mail and eDo you have
ventually
> the job stops. Do you have any comment on this? Shall I modify or do some
> additional stuffs here?
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Reserach Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Moblie Number: +44 (0) 7448233157
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Received on Thu Jun 20 2013 - 01:30:03 PDT
