AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Junmei Wang (junmwang_at_gmail.com)
Date: Fri Aug 15 2008 - 08:52:27 CDT

Hi John,
I have tested your molecule with the new code, it worked for me. Could you
send me your output? As to the cap of the side chain, the current version
does not have this function. But I can make it work in a couple days.

Best

Junmei

On Fri, Aug 15, 2008 at 1:12 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:

> Hi Junmei,
>
> I placed the new code and recompiled, but similar results.
> The TAIL_ATOM, HEAD_ATOM, OMIT_ATOM, first and second cap and residue atoms
> are all correct, but the mainchain atoms are wrong. This was using the same
> input as above.
>
> Distinct from the above matter but still about residuegen, all my current
> usage is about sidechain-sidechain binding for novel residues. For this, I
> need a charge group for the sidechain caps. Will I be able to specify
> sidechain cap charge groups in residuegen?
>
> cheers,
> John.
>
>
>
>
> On Wed, Aug 13, 2008 at 8:00 AM, Junmei Wang <junmwang_at_gmail.com> wrote:
>
>> 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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