AMBER Archive (2008)

Subject: AMBER: RE: amber help

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Apr 05 2008 - 22:25:19 CDT

Dear Rabindra

I am copying this to the amber mail reflector which is where such questions
should be directed so other can benefit from responses. Please see
http://www.ambermd.org for details on how to sign up.

To answer your question it looks like there may be a formatting problem with
your pdb file. E.g.

ATOM 31 P DA 1 2 -13.526 0.019 2.842 1.00 0.18
P

I believe that the extra 1 after the DA should not be there. I.e. it should
be:

ATOM 31 P DA 2 -13.526 0.019 2.842 1.00 0.18
P

Or also possibly:

ATOM 31 P A 2 -13.526 0.019 2.842 1.00 0.18
P

Note you will also need to rename the termini to be A5, A3 etc respectively.

See tutorial B1 of http://www.ambermd.org/tutorials/ for more details.

Good luck,
Ross

> -----Original Message-----
> From: rbajrach_at_kent.edu [mailto:rbajrach_at_kent.edu]
> Sent: Saturday, April 05, 2008 19:57
> To: ross_at_rosswalker.co.uk
> Subject: amber help
>
> Hi Dr. Walker,
> I am a graduate student from Kent state University. I am practicing to
> run amber8 on
> some pdb files. I tried to work with 2HY9.pdb file. But the
> problem is that when I try to creat the .prmtop and .inpcrd
> files it gives
> the following message
>
> WARNING: The unperturbed charge of the unit: -48.000000 is not zero.
> FATAL: Atom .R<DA 1>.A<H5' 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<H2' 35> does not have a type.
> FATAL: Atom .R<DA 1>.A<H2'' 36> does not have a type.
> FATAL: Atom .R<DA 2>.A<HO5' 37> does not have a type.
> FATAL: Atom .R<DA 2>.A<OP1 33> does not have a type.
> FATAL: Atom .R<DA 2>.A<OP2 34> does not have a type.
> ............................................
> ...............................................
> many more lines and the the .prmtop and .inpcrd files were
> empty that is
> they are not generated. Could you please suggest me what should I do
> inorder to generate the .prmtop and .inpcrd files without problem
>
> Thanking you in advance....
> rabindra
>

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