Re: Some problem on pair force calculation

From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Thu Jun 08 2006 - 20:40:11 CDT

Dear namd expert:
     I find if I replace "gb_2" with its corresponding value in the "*.top" file, it will be ok,and it seems that the "Include" statement in the "*.top" doesn't work.
    But it seems impossible to make all these inplacement manually since I don't know how the namd program read the gromacs "*.top" file.
        Can anyone give me any suggestion? Thank you a lot!

     Sting

==============

>namd-lHi all:
> I tried to compute the pair force using namd from a gromacs format trajectory(*trr). Following the user guide of namd,
>I builded the configure file(see below),but when I ran,some error occured:
> Info: GROMACS TOPO FILE TEQ2NO.top
> Info: GROMACS COOR FILE ../avg_wild_TEQ_md.pdb
> Required bondtype NL--H (function 2) not found.
> ------------- Processor 0 Exiting: Called CmiAbort -----------
>And NL--H was the first bond in top file.As one who had used gromacs should know that the gromacs top file looked like:
> ===========================
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> #include "s1360.itp"
> #include "ions.itp"
>
>[ moleculetype ]
>; Name nrexcl
>Protein_A 3
>
>[ atoms ]
>; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 NL 1 CYSH N 1 0.129 14.0067 ; qtot 0.129
> 2 H 1 CYSH H1 1 0.248 1.008 ; qtot 0.377
> 3 H 1 CYSH H2 1 0.248 1.008 ; qtot 0.625
> ..............
>[ bonds ]
>; ai aj funct c0 c1 c2 c3
> 1 2 2 gb_2
> 1 3 2 gb_2
>======================
> This file indicates that the force field of the atoms are included in another files(namely,ffG43a1.itp etc.), and also I had copied these files to local directory.
> Does anyone know the reason and any suggestion?
> Thank you in advance!
>
> Sting
>
>
> pair.conf
>==============================
>gromacs on
>grotopfile TEQ2NO.top
>coordinates ../avg_wild_TEQ_md.pdb
>
># initial config
>temperature 310
># output params
>outputname pairforce
>binaryoutput no
># integrator params
>timestep 2.0
># force field params
>#structure 1wdn_wb.psf
>#paraTypeCharmm on
>#parameters ../par_all27_prot_lipid.inp
>exclude scaled1-4
>1-4scaling 1.0
>switching on
>switchdist 10.0
>cutoff 12.0
>pairlistdist 13.5
>stepspercycle 10
># Atoms in group 1 have a 1 in the B column; group 2 has a 2.
>pairInteraction on
>pairInteractionFile ref.pdb
>pairInteractionCol B
>pairInteractionGroup1 1
>pairInteractionGroup2 2
># First frame saved was frame 1000.
>set ts 0
>coorfile open trr ../wild_TEQ_md.trr
># Read all frames until nonzero is returned.
>while { ![coorfile read] } {
> # Set firstTimestep so our energy output has the correct TS.
> firstTimestep $ts
> # Compute energies and forces, but don't try to move the atoms.
> run 0
> incr ts 100
>====================
>
>

= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        Sting
        stg1979_at_emails.bjut.edu.cn
          2006-06-09

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