Re: [AMBER] bug in respgen ?

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 26 Sep 2011 13:33:35 +0200

Thomas,

> So, bottom line: respgen produces an input according to the (old version of
> the) manual, but this is simply not what resp expects as input.

below are two R.E.D. Server jobs generated by using the R.E.D. Server
public account:
See http://q4md-forcefieldtools.org/REDS/faq.php#21


-1- first case: a single conformation (& a single orientation; we
usually involve $j orientations > 1) this means nmol = 1 in each RESP
input
See
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661.html

in the P2N file one requests to generate a central fragment for a
modified aminoacid for a single conformation $i = 1:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Mol_red1.p2n
REMARK
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
REMARK INTRA-MCC 0.0 | 20 21 22 23 24 25 | Remove
REMARK

- The RESP inputs without intra-molecular charge constraints:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/input1_m1
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/input2_m1
  & the corresponding mol2 file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/Mol_m1-o1.mol2 (molecule 1; conformation
1)

- The RESP inputs with intra-molecular charge constraints (i.e. to
generate the central fragment):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/input1_m1.sm
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/input2_m1.sm
  & the corresponding mol2 file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/Data-R.E.D.Server/Mol_m1-o1-sm.mol2
  & the corresponding java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF5pADFoGC7KADF8GAD8TMADFLj1QfBvWkKzDNADF/P3661/javaappletmol2-2.html

I run LEaP to check the total charge value for the central fragment:
[fyd.lynx Data-R.E.D.Server]$ cd P3661/Data-R.E.D.Server/
[fyd.lynx Data-R.E.D.Server]$ ll *.mol2
-rw-r--r--. 1 fyd fyd 2895 26 sept. 12:21 Mol_m1-o1.mol2
-rw-r--r--. 1 fyd fyd 1517 26 sept. 12:21 Mol_m1-o1-sm.mol2

[fyd.lynx Data-R.E.D.Server]$ tleap
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> qqq = loadmol2 Mol_m1-o1-sm.mol2
Loading Mol2 file: ./Mol_m1-o1-sm.mol2
Reading MOLECULE named AIB
> charge qqq
Total unperturbed charge: 0.000200
Total perturbed charge: 0.000200
> quit
        Quit

0.000200 i.e. 0.0000 +/- rounding off errors


-2- second case: two conformations (& a single orientation; we usually
involve $j orientations > 1) this means nmol = 2 in each RESP input
See
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662.html

in the P2N file one requests to generate a central fragment for a
modified aminoacid for two conformation2 $i = 2:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Mol_red1.p2n
REMARK
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
REMARK INTRA-MCC 0.0 | 20 21 22 23 24 25 | Remove
REMARK

- The RESP inputs without intra-molecular charge constraints:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/input1_m1
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/input2_m1
  & the corresponding mol2 files:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/Mol_m1-o1.mol2 (molecule 1; conformation
1)
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/Mol_m1-o2.mol2 (molecule 1; conformation
2)

- The RESP inputs with intra-molecular charge constraints (i.e. to
generate the central fragment):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/input1_m1.sm
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/input2_m1.sm
  & the corresponding mol2 files:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/Mol_m1-o1-sm.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/Data-R.E.D.Server/Mol_m1-o2-sm.mol2
  & the corresponding java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFIfcTUfQDADF5flv3ZnugUJUIUCWhyrN50/P3662/javaappletmol2-2.html

I run LEaP to check the total charge value of the fragment:
[fyd.lynx Data-R.E.D.Server]$ cd ../../P3662/Data-R.E.D.Server/
[fyd.lynx Data-R.E.D.Server]$ ll *.mol2
-rw-r--r--. 1 fyd fyd 2895 26 sept. 12:21 Mol_m1-o1.mol2
-rw-r--r--. 1 fyd fyd 1517 26 sept. 12:21 Mol_m1-o1-sm.mol2
-rw-r--r--. 1 fyd fyd 2895 26 sept. 12:21 Mol_m1-o2.mol2
-rw-r--r--. 1 fyd fyd 1517 26 sept. 12:21 Mol_m1-o2-sm.mol2
[fyd.lynx Data-R.E.D.Server]$ tleap
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> qqq = loadmol2 Mol_m1-o1-sm.mol2
Loading Mol2 file: ./Mol_m1-o1-sm.mol2
Reading MOLECULE named AIB
> charge qqq
Total unperturbed charge: -0.000200
Total perturbed charge: -0.000200
> quit
        Quit

  -0.000200 i.e. 0.0000 +/- rounding off errors

I think all is OK here...

  ---

In your case you can push one step further & generate the force field
libraries for the Central, N-terminal and C-terminal fragments as well
as for the dipeptide molecule by only providing a single P2N file for
the dipeptide in a single R.E.D. IV job.
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
   versus
      http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

regards, Francois



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Received on Mon Sep 26 2011 - 05:00:02 PDT