AMBER Archive (2009)

Subject: Re: [AMBER] non standard residue

From: FyD (
Date: Tue Jul 14 2009 - 15:01:32 CDT

Dear Eduardo,

> I fixed the problem, it appears that
> was unable to extract the resp points from the GAMESS output.

You did not say you use GAMESS-US ;-)

When using GAMESS-US, R.E.D. gets the MEP points from the .dat (punch)
file (& not from the .log file!). This .dat file has to be moved from
the scratch directory by R.E.D.

This means you need to modify your "rungms" script such as it is
described in the R.E.D.-II manual end of page 7.

You need to set:
setenv PUNCH $SCR/$JOB.dat

> I extracted the resp points from a GAUSSIAN output, placed them
> on a file esp.dat. I then make copies to replace the espot_m1 files,
> changing writing permissions,
> this way my replacement was used instead of that produced by RED, that
> I was able to run
> again using the previously produced GAMESS output, this time with
> resp points.

You should not need to do that. All is done automatically...

> Is this a bug or my local machines have a grudge against me?.

Just modify your "rungms" script according to what is written end of
page 7 in the RED-II manual.

regards, Francois

>> Dear Francois.
>> I have been trying to use the RED program to obtain charges for a
>> "new" residue (just a deprotonated THR),
>> and so far RED fails at this stage:
>> MEP(s) is/are being computed for molecule 1 ... [ OK ]
>> See the file(s) "JOB2-gam_m1-1-(X).log"
>> The RESP-A1 charges are being derived for molecule 1 ... [ FAILED ]
>> Is this because I have no charges in the input?.
>> What can I change to make the program work?.
>> I am sorry if the question is way too general, but I am lost in here,
>> any input would be appreciated.
>> Eduardo Mendez

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