Re: [AMBER] reaidt.f problem

From: Premila Samuel Mohan Dass <>
Date: Sun, 4 Mar 2018 20:54:10 +0000

Here is an example on how to prepare input for Amber’s resp:
$AMBERHOME/bin/resp -O -i -t 1u7r.chg -p 1u7r.pch -o testresp.out -q 1u7r.qin -e esp_espgen.esp

You get the esp_espgen.esp file using Amber’s espgen on your gaussian log file. To prepare the .in file, you can use Amber’s respgen. The .in file is used to specify the atomic numbers and whether the charges are restrained for specific atoms. In line 9 of the file, the total charge of the system and total number of atoms are specified in the first and 2nd column. In the following lines, the first column has each atomic number corresponding to each of the atoms of residues prepared for Gaussian input. In the second column, if an atom charge is restrained to a specific value to be referred to a .qin file prepared, you give a value of -1. If the charge is allowed to be free-floating, you give a value of 0 in the second column, and if the charge derivation is constrained with another atom to be the same as in the case for methyl hydrogens, then the number of the first atom constrained is given.

You also prepare the qin file specifying the reference charges for each atom for beginning of the fitting. The qin file has a specific format of 8 atoms separated by spaces per line. The format is similar to .chg output you will get.

Some references for resp fitting are below and you can see how they prepared the files required for Amber’s resp:

Using RED is probably simpler however.

Premila Samuel

On Mar 4, 2018, at 3:26 PM, Premila Samuel Mohan Dass <<>> wrote:

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You can use espgen, Amber program, to extract ESP fit center from the gaussian output file. Gaussian does not calculate RESP charges, have to use Amber resp program to do that.
For example, use: espgen -i gaussian.log -o esp_espgen.esp

Then prepare the other input files for use with Amber’s resp program with Amber’s respgen.

Premila P. Samuel, Ph.D.
Post-Doctoral Associate,
Dr. David Case research group,
Center of Proteomics,
Rutgers University,
174 Frelinghuysen Road,
Piscataway, NJ 08854

On Mar 4, 2018, at 3:19 PM, Barış Kurt <<><>> wrote:

++and also I calculated RESP charges with gaussian09 now I don't know how
to import them into AMBer as a dat files?

2018-03-04 23:11 GMT+03:00 Barış Kurt <<><>>:

Sir, of course first I compiled fortran (otherwise it would be impossible
to get "syntax error") . I don't want to use RED I have no time for
learning another program.

2018-03-04 16:41 GMT+03:00 David A Case <<><>>:

On Sun, Mar 04, 2018, Barış Kurt wrote:

I found readit.f on amber web site and copied pasted it but when I try
run it I got

syntax error near unexpected token `('

What do you mean by "try to run it"? This is Fortran program, which
would need to be compiled first. Can you say exactly what you did.

But further, this file is 20 years old, and not a part of Amber anymore.
What do you expect it to do? What problem are you trying to solve?

If you want to do RESP calculations, I'd suggest trying the R.E.D. web
site (see pointers at<><>).


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Received on Sun Mar 04 2018 - 13:00:02 PST
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