AMBER Archive (2009)

Subject: Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Aug 31 2009 - 15:10:52 CDT

Dear Jia Xu,

You might try R.E.D. where RESP inputs are automatically built from
the P2N file format.

The P2N file format is described @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3

For charge derivation of aminoacid fragments, see for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#13

See R.E.D. Server tutorial & charge derivation of aminoacid fragments:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

regards, Francois

> Dear amber users,
>
> I am using amber9 and trying to generate topology files of
> 4-hydroxyl-proline (PR4) under the guidance of tutorial (
> http://ambermd.org/antechamber/pro4.html).
>
> From step1 to step3, everything looks fine.
>
> However, in step4, the command *respgen -i pro4a.mol2 -o pro4-step1.respin
> -f resp1 *is supposed to generate a respin file as follows:
>
>
>
> Resp charges for organic molecule
>
>
>
> &cntrl
>
>
>
> nmol = 2,
>
> ihfree = 1,
>
> ioutopt = 1,
>
>
>
> &end
>
> 1.0
>
> Resp fit for 4-OH-PRO
>
> 0 27
>
> 1 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 8 0
>
> 7 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 8 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 6 0
>
> 8 0
>
> 7 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 1 0
>
> 1 0
>
>
>
> 1.0
>
> Resp fit for 4-OH-PRO
>
> 0 27
>
> 1 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 8 0
>
> 7 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 8 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 6 0
>
> 8 0
>
> 7 0
>
> 1 0
>
> 6 0
>
> 1 0
>
> 1 0
>
> 1 0
>
> 1 0
>
>
>
>
>
> 2
>
> 1 1 2 1
>
> 2
>
> 1 2 2 2
>
> 2
>
> 1 3 2 3
>
> 2
>
> 1 4 2 4
>
> 2
>
> 1 5 2 5
>
> 2
>
> 1 6 2 6
>
> 2
>
> 1 7 2 7
>
> 2
>
> 1 8 2 8
>
> 2
>
> 1 9 2 9
>
> 2
>
> 1 10 2 10
>
> 2
>
> 1 11 2 11
>
> 2
>
> 1 12 2 12
>
> 2
>
> 1 13 2 13
>
> 2
>
> 1 14 2 14
>
> 2
>
> 1 15 2 15
>
> 2
>
> 1 16 2 16
>
> 2
>
> 1 17 2 17
>
> 2
>
> 1 18 2 18
>
> 2
>
> 1 19 2 19
>
> 2
>
> 1 20 2 20
>
> 2
>
> 1 21 2 21
>
> 2
>
> 1 22 2 22
>
> 2
>
> 1 23 2 23
>
> 2
>
> 1 24 2 24
>
> 2
>
> 1 25 2 25
>
> 2
>
> 1 26 2 26
>
> 2
>
> 1 27 2 27
>
>
>
> Unfortunately, the respin file I generated using the same command
> looks as follows:
>
>
>
> Resp charges for organic molecule
>
>
>
> &cntrl
>
>
>
> nmol = 1,
>
> ihfree = 1,
>
> ioutopt = 1,
>
>
>
> &end
>
> 1.0
>
> Resp charges for organic molecule
>
> 0 0
>
>
>
> My mol2 files and Gaussian output files were downloaded from the
> tutorial website, and I did exactly what the tutorial required.
>
>
>
> Could someone please help me on that?
>
> Thanks in advance!
>
> --
> Jia Xu

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