[gmx-users] .top file after using amber2gromacs
jalemkul at vt.edu
Mon Mar 3 05:34:11 CET 2014
On 3/2/14, 11:24 PM, Chetan Mahajan wrote:
> 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
Please refer to manual section 5.7.1, where each of these terms is explained
after the urea.top example.
> * 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.
Charge and mass information in [atomtypes] is indeed over-written by whatever is
found in [atoms]. You can always confirm what has been used by obtaining the
grompp-processed topology with grompp -pp or by using gmxdump on the .tpr file.
> * 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
Different force fields work in different ways, so the Gromacs file format is
standard across all the different force fields. Since there are generally fewer
types of bonded interactions, bonded types are a subset of nonbonded types.
Sometimes there are no differences, as is the case here. If a force field uses
separate bonded and nonbonded types, that just means the bonded types are an
interpretation of the atom types used within ffbonded.itp. The ptype column is
particle type - A for atoms, S for shells, V for virtual sites. The last two
columns are a comment, likely the original AMBER parameters so you can verify
the unit conversion.
> (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)*
cgnr = charge group number
nr = atom number
> nr type resi res atom cgnr charge mass ; qtot
> 1 Ti 1 iO2 TI 1 1.691002 47.86700 ; qtot 1.691
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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