[gmx-users] .top file after using amber2gromacs

Chetan Mahajan chetanvm10 at gmail.com
Mon Mar 3 05:24:15 CET 2014

Hi All

I have gromacs files generated using acpype tool acting on Amber files
I need to know the meaning of certain terms in that *.top file (email with
attachment of .top file got blocked due to attachment). Unfortunately, I
can't find on the web, any material regarding that. It would be great, if
anyone could comment on the following.

*1. What is the meaning of terms under defaults option at the top of the
file (pasted below)?*

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ   fudgeQQ
     1                    2                 yes                  0.5

* 2a. ** Is atomtypes section needed? (sample .top file on gromacs website
does not have it) (pasted after 2b question)**In this atomtypes section,
the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a
simulation with these places zero be a valid simulation **?* My guess is
yes. THis is since, corresponding values are available later in atoms
section. The purpose of asking this question is that I have to be sure of
the runs I have made, that nothing has gone wrong in having those zeros.

* 2b.I see several enigmatic terms such as bond type p type, Amb. Can you
explain these terms, if they are necessary at all? Why last two columns for

(part of the data for both 2a and 2b pasted below)
[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma         epsilon
     Ti       Ti              0.00000  0.00000   A     1.39461e-01
6.08772e-02 ; 0.78  0.0145
    OT       OT           0.00000  0.00000   A     2.87832e-01
8.29687e-02 ; 1.62  0.0198
    HW       HW          0.00000  0.00000   A     0.00000e+00   0.00000e+00
; 0.00  0.0000

*4.WHat is cgnr? how is it different from nr? (it appears in atoms section,
example below)*

 nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
     1   Ti     1   iO2    TI    1     1.691002     47.86700 ; qtot 1.691


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