Dear David:
Thank you very much for replying my email, under your help, I fixed the problem I showed. you are right about the "modern" and "old" problem, after changing "OP2" to "o2p", part of my problem have been solved. but the problem I haven't shown you still exist:
"FATAL: Atom .R<DA 1>.A<HO5' 33> does not have a type.
FATAL: Atom .R<DA 1>.A<H5' 34> does not have a type.
FATAL: Atom .R<DA 1>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DA 1>.A<H2' 36> does not have a type.
FATAL: Atom .R<DA 1>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DT 2>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 2>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 2>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 2>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 3>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 3>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 3>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 3>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 4>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 4>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 4>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 4>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 5>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 5>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 5>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 5>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 6>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 6>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 6>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 6>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DG 7>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 7>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 7>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 7>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DT 8>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 8>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 8>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 8>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 9>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 9>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 9>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 9>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 10>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 10>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 10>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 10>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DC 11>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 11>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 11>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 11>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DG 12>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 12>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 12>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 12>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DC 13>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 13>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 13>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 13>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DG 14>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 14>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 14>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 14>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DC 15>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 15>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 15>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 15>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DC 16>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 16>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 16>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 16>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DC 17>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 17>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 17>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 17>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DT 18>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 18>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 18>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 18>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 19>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 19>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 19>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 19>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 20>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 20>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 20>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 20>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DC 21>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 21>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 21>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 21>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DT 22>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 22>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 22>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 22>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DC 23>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 23>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 23>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 23>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DA 24>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 24>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 24>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 24>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 25>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 25>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 25>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 25>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 25>.A<HO3' 37> does not have a type.
FATAL: Atom .R<DT 26>.A<HO5' 33> does not have a type.
FATAL: Atom .R<DT 26>.A<H5' 34> does not have a type.
FATAL: Atom .R<DT 26>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DT 26>.A<H2' 36> does not have a type.
FATAL: Atom .R<DT 26>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DT 27>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 27>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 27>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 27>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DG 28>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 28>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 28>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 28>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DA 29>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 29>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 29>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 29>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DG 30>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 30>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 30>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 30>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DA 31>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 31>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 31>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 31>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 32>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 32>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 32>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 32>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 33>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 33>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 33>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 33>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DG 34>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 34>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 34>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 34>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DG 35>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 35>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 35>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 35>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DG 36>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 36>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 36>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 36>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DC 37>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 37>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 37>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 37>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DG 38>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 38>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 38>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 38>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DC 39>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 39>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 39>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 39>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DG 40>.A<H5' 34> does not have a type.
FATAL: Atom .R<DG 40>.A<H5'' 35> does not have a type.
FATAL: Atom .R<DG 40>.A<H2' 36> does not have a type.
FATAL: Atom .R<DG 40>.A<H2'' 37> does not have a type.
FATAL: Atom .R<DA 41>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 41>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 41>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 41>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 42>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 42>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 42>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 42>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 43>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 43>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 43>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 43>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DC 44>.A<H5' 31> does not have a type.
FATAL: Atom .R<DC 44>.A<H5'' 32> does not have a type.
FATAL: Atom .R<DC 44>.A<H2' 33> does not have a type.
FATAL: Atom .R<DC 44>.A<H2'' 34> does not have a type.
FATAL: Atom .R<DT 45>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 45>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 45>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 45>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 46>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 46>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 46>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 46>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 47>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 47>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 47>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 47>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 48>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 48>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 48>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 48>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DA 49>.A<H5' 33> does not have a type.
FATAL: Atom .R<DA 49>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DA 49>.A<H2' 35> does not have a type.
FATAL: Atom .R<DA 49>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 50>.A<H5' 33> does not have a type.
FATAL: Atom .R<DT 50>.A<H5'' 34> does not have a type.
FATAL: Atom .R<DT 50>.A<H2' 35> does not have a type.
FATAL: Atom .R<DT 50>.A<H2'' 36> does not have a type.
FATAL: Atom .R<DT 50>.A<HO3' 37> does not have a type"
could you please tell me the "old" code for these"H2'34"thing? thank you very much and wish you have a good day!
------------------ 原始邮件 ------------------
发件人: "David A Case";<case.biomaps.rutgers.edu>;
发送时间: 2015年2月4日(星期三) 晚上9:11
收件人: "AMBER Mailing List"<amber.ambermd.org>;
主题: Re: [AMBER] seek help
On Wed, Feb 04, 2015, 新生大侠 wrote:
> Dear AMBER users: I am an amber user in China, and I am getting the
> following error while running xleap in AMBER10
> :"FATAL: Atom .R<DT 2>.A<OP1 33> does not have a type.
> FATAL: Atom .R<DT 2>.A<OP2 34> does not have a type.
What leaprc file are you using? Since the release of Amber10, the PDB (and
the Amber programs) have changed the names of the oxygens bonded to P from
"O1P/O2P" (old nomenclature) to "OP1/OP2" (new nomenclature). I'm guessing
(based on limited evidence) that you are using a "modern" PDB file but an
"old" library.
I recommend that you update to AmberTools14 and see if that helps. I big
added plus is that you will also get access to much better force fields for
nucleic acids: Amber10 was released in 2008, and a lot has changed since then.
...dac
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Received on Wed Feb 04 2015 - 07:00:03 PST
