AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Thu Jul 31 2008 - 22:21:54 CDT

Just went back to try the prepgen step again using the prepgen from amber8.
This one works! It changes the charge values for the truncated molecule, and
the overall charge of the truncated molecule really is zero. The other
prepgens falsely claim that the charge of the truncated molecule is zero.

On Fri, Aug 1, 2008 at 11:59 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:

> Same problem here, have also tried antechamber-1.27 with same result.
>
>
>
>> 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.
>>
>>
>

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