THank you jason an David, you have do a lot good to my work. I did not update the AMBER TOOLs because I am doing the comparing work, In the papers I have read, the author used AMBER 10 to do the work. So I have to do just like him. I used amber 10 to model the DNA structure, and I have got the primary structure successfully. The next work I have to do is doing MD to get the equilbrium structure. However, when I wanted to get the prmtop file of the DNA using tleap leaprc.ff99sb, something goes wrong: some atoms on DNA can not be recognized.
When I get into the tleap leaprc.ff99sb, the code I have type is" dna1 = loadpdb nuc.pdb" , then the pdb was loaded and some atoms were added automatically:
"Created a new atom named: H2' within residue: .R<DA 48>
Created a new atom named: H2'' within residue: .R<DA 48>
Created a new atom named: H5' within residue: .R<DA 49>
Created a new atom named: H5'' within residue: .R<DA 49>
Created a new atom named: H2' within residue: .R<DA 49>
Created a new atom named: H2'' within residue: .R<DA 49>
Created a new atom named: H5' within residue: .R<DT 50>
Created a new atom named: H5'' within residue: .R<DT 50>
Created a new atom named: H2' within residue: .R<DT 50>
Created a new atom named: H2'' within residue: .R<DT 50>
Created a new atom named: HO3' within residue: .R<DT 50>
total atoms in file: 1588
Leap added 206 missing atoms according to residue templates:
6 Heavy
200 H / lone pairs
The file contained 204 atoms not in residue templates" (part of the report)
Then, when I want to save the prmtop file, I typed"saveamberparm dna1 ployAT_vac.prmtop ployAT_vac.inpcrd"
then the fatal error comes:"Checking Unit.
WARNING: The unperturbed charge of the unit: -50.000000 is not zero.
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.
Failed to generate parameters
Parameter file was not saved."
Could you please tell me what could I do other than updating my AMBER TOOLs? I really appreciate your reply! hope you all have a good day!
jinzheng wang
------------------ 原始邮件 ------------------
发件人: "jason.swails";<jason.swails.gmail.com>;
发送时间: 2015年2月5日(星期四) 凌晨0:01
收件人: "AMBER Mailing List"<amber.ambermd.org>;
主题: Re: [AMBER] 回复： seek help
On Wed, Feb 4, 2015 at 9:55 AM, 新生大侠 <390155909.qq.com> wrote:
> 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.
> [snip]
>
> 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!
>
Do you have a reason not to update to AmberTools 14 and use a modern force
field? If you do, your PDB file will work without having to modify it, AND
you will get better force fields. It will be difficult to get a simulation
using old force fields accepted in peer-reviewed journals when demonstrably
superior alternatives exist.
That said, the atom names in the template are in the
$AMBERHOME/dat/leap/lib library files (probably something like
all_nucleic94.lib, or something). Again, use of these old force fields is
strongly discouraged (unless you are doing some type of comparative study
to show their deficiencies) -- you would be much better off downloading the
latest version of AmberTools and using the latest force fields there
instead.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 04 2015 - 19:30:03 PST
