AMBER Archive (2009)

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

From: Jia Xu (xujia.ruc_at_gmail.com)
Date: Sun Aug 30 2009 - 02:46:18 CDT

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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