Kamali,
See
http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
vs
http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
"R.E.D. Server does not tolerate such structures":
what does it mean?
Prepare your input file(s) & run the server - look at the error
message generated if the program does not end correctly & request for
help
http://q4md-forcefieldtools.org/REDS/faq.php#5.
R.E.D. will handle your molecule(s)... The problems are only:
- how to analyze the error messages generated?
- how to use the data generated?
regards, Francois
> Thanks for the reminder! I am also interested in generating parameters for
> more unusual moieties, such as the 2'3' cyclic phosphate product of
> ribozyme cleavage, and was thinking that perhaps the RED server doesn't
> tolerate such structures? If I am mistaken, however, I might try the RED
> server again.
> On Sun, Oct 13, 2013 at 10:05 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Kamali,
>>
>> if you have an open valency in your molecular system and/or want to
>> generate a molecular fragment you might try R.E.D. Server at
>> q4md-forcefieldtools.org
>>
>> regards, Francois
>>
>>
>> > Thank you very much, Dr. Case; I wasn't aware that the "-nc" flag was
>> only
>> > for amb1-bcc calculations. Would you be able to tell me what the warning
>> > means? It seems to me that antechamber is misinterpreting the fact that
>> the
>> > N1 atom now only has 2 bonds as an indication of incomplete valence, but
>> > I'm not sure how much this will distort the resulting charges, and also
>> if
>> > there's a way to let antechamber know that the "incomplete valency" is
>> > intentional.
>>
>>
>>
>> > On Sat, Oct 12, 2013 at 11:39 AM, David Case <dacase.rci.rutgers.edu>
>> wrote:
>> >
>> >>
>> >>
>> >> > On Oct 12, 2013, at 10:22 AM, Kamali Sripathi <ksripath.umich.edu>
>> >> wrote:
>> >> >
>> >> >
>> >> > I am using Gaussian and antechamber to parameterize an N1-unprotonated
>> >> > guanine for RNA. I initially generated a prepc file while forgetting
>> to
>> >> add
>> >> > the "-nc -1" flag. I re-ran the calculations using this flag, but the
>> two
>> >> > resulting prepc files are the same. I have compared prepc files for
>> other
>> >> > molecules with and without the "-nc" flag and found the same thing
>> >> happen.
>> >>
>> >> The -nc flag only applies to am1-bcc charge calculations. You provided
>> >> the net charge to Gaussian in its inout file.
>> >>
>> >> ...dac
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Received on Sun Oct 13 2013 - 10:00:02 PDT
