AMBER Archive (2007)

Subject: Re: AMBER: Re: antechamber problem

From: sanket deshmukh (sanket.deshmukh_at_ucd.ie)
Date: Wed Nov 28 2007 - 08:05:37 CST

Thanks for your guidance!

Sanket A Deshmukh
Research Student
School of Chemical and Bioprocess Engineering,
Engineering and Material Science Building,
University College Dublin,
Dublin-04, Ireland.
Mob. +353 862132132.
Off. +353 17061866.

----- Original Message -----
From: Junmei Wang <junmwang_at_yahoo.com>
Date: Tuesday, November 27, 2007 5:58 pm
Subject: AMBER: Re: antechamber problem
To: "David A. Case" <case_at_scripps.edu>, amber_at_scripps.edu

> The format of the pdb file is not very correct. The correct one is
> attached with this email. I think the new program, acdoctor.c in
> amber10 can detect this kind of problem in the future. In my
> opinion, the pdb format, although widely used, is not a very good
> molecular format, antechamber has to read this format by column not
> by field. Therefore, the atom names, atom ids, residue names,
> residue ids, coordinates must in their designated columns.
>
> Best
>
> Junmei
>
>
>
> ----- Original Message ----
> From: David A. Case <case_at_scripps.edu>
> To: amber_at_scripps.edu
> Cc: junmwang_at_yahoo.com
> Sent: Friday, November 23, 2007 8:40:21 PM
> Subject: antechamber problem
>
> On Fri, Nov 23, 2007, sanket deshmukh wrote:
>
> > I have modified the structure and used only one molecule (26
> atom the
> > way you suggested to me). It is relaxed now but still I am facing
> the> same problem regarding the connectivity.
>
> [The "same problem" is that antechamber can't assign atom and bond
> types.]
> I'll admit this is wierd. I'm cc-ing to Junmei to see if he can
> spot the
> problem. Here is the input pdb file that antechamber can't handle:
>
>
> ATOM 1 C 1 7.397 10.474 12.292
> ATOM 2 H11 2 7.849 10.392 13.319
> ATOM 3 H12 3 7.130 9.435 11.964
> ATOM 4 C1 4 8.397 11.095 11.349
> ATOM 5 H1 5 8.716 12.098 11.723
> ATOM 6 H2 6 9.298 10.440 11.274
> ATOM 7 H3 7 7.964 11.224 10.325
> ATOM 8 C2 8 6.159 11.307 12.420
> ATOM 9 O1 9 5.923 12.116 13.318
> ATOM 10 O2 10 5.093 11.213 11.552
> ATOM 11 C3 11 5.191 10.460 10.350
> ATOM 12 H4 12 4.319 9.752 10.378
> ATOM 13 H5 13 6.151 9.892 10.260
> ATOM 14 C4 14 5.030 11.417 9.168
> ATOM 15 H6 15 4.468 10.917 8.337
> ATOM 16 H7 16 4.500 12.351 9.491
> ATOM 17 O3 17 6.353 11.728 8.728
> ATOM 18 C5 18 6.495 12.614 7.683
> ATOM 19 O4 19 7.680 12.833 7.431
> ATOM 20 C6 20 5.289 13.166 6.994
> ATOM 21 H14 21 4.726 12.309 6.535
> ATOM 22 H15 22 4.620 13.647 7.757
> ATOM 23 C7 23 5.662 14.168 5.931
> ATOM 24 H8 24 6.395 13.724 5.215
> ATOM 25 H9 25 4.750 14.484 5.371
> ATOM 26 H10 26 6.134 15.069 6.393
> CONECT 1 4 3 8 2
> CONECT 2 1
> CONECT 3 1
> CONECT 4 7 5 1 6
> CONECT 5 4
> CONECT 6 4
> CONECT 7 4
> CONECT 8 10 1 9
> CONECT 9 8
> CONECT 10 11 8
> CONECT 11 13 12 10 14
> CONECT 12 11
> CONECT 13 11
> CONECT 14 16 17 15 11
> CONECT 15 14
> CONECT 16 14
> CONECT 17 18 14
> CONECT 18 20 19 17
> CONECT 19 18
> CONECT 20 23 21 22 18
> CONECT 21 20
> CONECT 22 20
> CONECT 23 24 25 20 26
> CONECT 24 23
> CONECT 25 23
> CONECT 26 23
> END
>
> ....dac
>
>
>
>
>
>
>
>
____________________________________________________________________________________Never
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>
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