AMBER Archive (2005)

Subject: Re: AMBER: Making topology files of big moleucles in antechamber

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Fri Mar 18 2005 - 10:48:02 CST

Thank you very much for your suggestion.
I'm new to AMBER, and I cannot understand some of your suggestions.
What you mean is that I can create topology files of individual
residues of dendrimer, and then can combine those topologies by using
leap?? If so, can I combine topologies by using leap?
Could you explain more details about your advice?
Thanks for your help in advance.

best,
Hwankyu.

On Mar 17, 2005, at 2:48 PM, Melinda Layten wrote:

> Since a quick google search defined a dendrimer as a branched polymer,
> you can create "residues" based on the polymer subunit instead of
> trying to define the whole molecule in one go. You can then build up
> the subunits using leap.
>
>
> On Thu, 17 Mar 2005 11:09:06 -0500, Hwankyu Lee <leehk_at_umich.edu>
> wrote:
>> Dear amber-users,
>>
>> I'm trying to make topology of big molecules(dendrimer;atom numbers >
>> ~5000) by
>> using antechamber. Although antechamber is suitable for small
>> molecules,
>> antechamber is the only tool to create topology files for amber
>> package. So,
>> I'm trying to make topology of dendrimer by following manuals and
>> searching
>> amber forum.
>>
>> Some answers in the forum suggested to increase MAXATM in define.h and
>> divcon.dim and use '-j 5' and so on.
>> So, I increased some parameters in define.h like below.
>> --------------------------
>> # define COLORTEXT "YES"
>> # define REDUCEFACTOR 1
>> # define PI 3.1415926
>> # define MAXCHAR 6000
>> # define MAXATOM 6000
>> # define MAXBOND 6000
>> # define MAXRING 1000
>> # define MAXGAS 500 /*maximum gasiteger parameters*/
>> /*
>> For MAXRING, no dynamic memory applied since the actuall number is
>> determined
>> using a recursive function. However, for small and middle-sized
>> molecules,
>> it is unlikely that the ring num is larger than 1000
>> */
>> # define MAXCYCLE 100
>> # define OUTPUTSTEP 10
>> # define MAXTWIST 10
>> # define ECSLONG 2
>> # define COSCUT 120
>> # define DEGRAD 3.1415926/180
>> # define VDWIDIST 10
>> # define ESIDIST 14
>> # define THETACUT 15
>> # define CUBE 2.0
>> # define MAXWILDATOM 20
>> # define MAXSCHAIN 100
>> # define MAXCES 20
>> # define MAXBEED 20
>> # define MAXATOMTYPE 250
>> # define MAXVASTATE 6000
>> # define PSCUTOFF 7
>> # define MAX_CES_BOND 100
>> ---------------------------
>> Also, in divcon.dim file, I modified that into "MAXATM=6000".
>> The parametes in divcon.dim are shown in below.
>> --------------
>> MAXIMUM NUMBER OF ATOMS:
>> PARAMETER (MAXATM =6000)
>> C
>> C FRACTION OF ATOMS THAT ARE EXPECTED TO BE HEAVY:
>> PARAMETER (FHEAVY = 0.50)
>> C
>> C MAXIMUM NUMBER OF ATOM PAIRS (INFINITE CUTOFF):
>> PARAMETER (MXPAIR =50000)
>> C
>> C MAXIMUM NUMBER OF ATOM PAIRS THAT ARE STORED FOR OFF-DIAGONAL
>> C INTERACTIONS IN FOCK, 1-ELECTRON, AND DENSITY MATRICES:
>> PARAMETER (MBPAIR =400000)
>> C
>> C MAXIMUM NUMBER OF RESIDUE-BASED ATOM PAIRS (USED FOR AUTOMATIC
>> C SUBSETTING, 5 ANGSTROM CUTOFF) (CODE=M):
>> C [ SET TO ONE IF CLUSTER-BASED SUBSETTING IS NOT USED ]
>> PARAMETER (MXPRES = 10000)
>> C
>> C MAXIMUM NUMBER OF SUBSYSTEMS:
>> PARAMETER (MAXSUB =600)
>> C
>> C STORAGE FOR SUBSYSTEM ATOM LISTS:
>> PARAMETER (MSLIST =350000)
>> C
>> C STORAGE FOR ALL SUBSYSTEM EIGENVALUES (CODE=L):
>> PARAMETER (MSVAL =350000)
>> C
>> C SCRATCH STORAGE FOR MAXIMUM NUMBER OF ORBITALS IN A SUBSYSTEM
>> (CODE=L)
>> C [SEE ALSO MSRORB PARAMETER]:
>> PARAMETER (MSORB =2000)
>> ----------------------------------
>>
>> Then, when I used "antechamber -i XXX.pdb -fi pdb -o XXX.prepin -fo
>> prepi -c bcc
>> -s 2 -j 5 -nc 128", it took so long time, and then show this error
>> like below.
>> ---------------------
>> db -o g5ace80.prepin -fo prepi -c bcc -s 2 -j 5 -nc 128
>> Running: /home/leehk/local/amber8/exe/bondtype -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o A
>> NTECHAMBER_BOND_TYPE.AC -f ac -j part
>>
>> Running: /home/leehk/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0
>> -o
>> ANTECHAMBER_AC.AC -p gaff
>>
>> Total number of electrons: 18094; net charge: 128
>>
>> Running: /home/leehk/local/amber8/exe/divcon
>> Unable to find mopac charges in divcon.out
>> ------------------------------
>>
>> When I used antechamber with small molecules, it nicely worked. So, I
>> think that
>> there is no problem with antechamber in my computer. So, it looks
>> like this
>> problem comes from size of molecules.
>> How can I use antechamber for big molecules?? If it is impossible to
>> do that,
>> how can I generate topology of big molecules? If I cannot generate
>> topology of
>> big molecules, is it impossible to simulate big molecules in amber
>> package?
>>
>> Thanks for your help in advance.
>>
>> best,
>> Hwankyu.
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