AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Aug 12 2008 - 17:30:45 CDT

Hi, John
I think there is a bug in residuegen to identify the main chain atoms. I
have fixed it. Please find the attached residuegen.c and recompile the
program. All the best

Junmei

On Mon, Aug 11, 2008 at 2:10 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:

> 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_at_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_at_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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