Dear Francois,
I have already registered and downloaded the software, and I will use
it.
Thank you for your kind reply!
Jia Xu
On Tue, Sep 1, 2009 at 4:10 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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Received on Wed Sep 02 2009 - 23:07:04 PDT
