Re: AMBER: Prepgen

From: Grange Hermitage <ghermitage.gmail.com>
Date: Mon, 11 Aug 2008 16:40:00 +0930

Hi Junmei,

There is an error in residuegen (which is why I used prepgen).
After separating the caps correctly, residuegen then proceeds to wrongly
identify the mainchain.
Relevant files are attached.

cheers,
   John.



On Wed, Aug 6, 2008 at 1:20 AM, Junmei Wang <junmwang.gmail.com> wrote:

> Hello Everyone,
> There is a bug with prepgen to do the charge correction. Please correct it
> and recompile the program. To generate non-standard amino acid-like
> residues, it is highly recommended to use residuegen, which can handle
> single/multiple conformations and easier to use. If no charge correction was
> needed or you used residuegen to generate non-standard residues, this bug
> should not affect your results.
>
> AmberTools-1.2 - Line 1114 of prepgen.c
> Amber10 - Line 1112 of prepgen.c
> Amber9 -Line 1043 of prepgen.c
>
> Change "if (omitnum > 0 && charge >= 9990.)" to "if (omitnum > 0 && charge
> <= 9990.)"
>
> All the best
>
> Junmei
>
>
>
> On Wed, Jul 30, 2008 at 3:58 AM, Heikki Salo <hssalo.gmail.com> wrote:
>
>> Dear Amber users,
>>
>> I have had exactly same problems as mentioned by Ojha. I tried to assign
>> charges to my modified amino-acid but after using the prepgen, to remove the
>> ACE and NME residues, the charge of the center amino-acid was not zero.
>>
>> I faced the same problem when I followed the antechamber tutorial 2. (on
>> page http://amber.scripps.edu/antechamber/pro4.html). After using prepgen
>> the charges did not match with the prepi file on the tutorial page. I
>> noticed that the charges were not changed from the earlier ac file.
>>
>> I took a look at the source code of prepgen.c. I noticed that in the main
>> program on line 1114 there is an following if statement:
>> "if (omitnum > 0 && charge >= 9990.) {"
>>
>> After this follow the lines, where the charges of the atoms not in the
>> omit list are calculated.
>>
>> If I got it right, the charge variable is the CHARGE on mainchain.dat
>> file. Could there be a bug on this line, which could cause the problem. When
>> would the charge variable get values over 9990? Please correct me if I
>> intepreted the code completely wrong.
>>
>> The version of antechamber, which I am using is the one included in
>> Ambertools-1.2.
>>
>> H. Salo
>>
>>
>>
>>
>



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Received on Wed Aug 13 2008 - 06:07:17 PDT
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