AMBER Archive (2009)

Subject: Re: [AMBER] RE:xleap problem

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Mon Jan 26 2009 - 15:40:22 CST

Dear Dodson,

*Thank* *you* *very* *much* for *your* attention. I became very happy to
your interest. I'm now making a summary for my study : I'm trying to get the
prmtop and inpcrd files for my n-alkanes simulations with using xleap. My
leap.log file is in below. I want to do MD simulations for 100 n-dodecane
 molecules. I'm now on Windows so I can only use rar or zip format for
compressing files. I'm so sorry for this. I attached the related files to
the mail. I used packmol in order to get my pdb file that includes 100
n-dodecane molecules. I added TER cards between each seperate n-dodecane
molecule with using a script. You can examine my packmol pdb file attached
to the mail. Then I started the minimization, but the min. progress stopped
and I got this error: Box parameters not found in inpcrd file! in min.out
file. So I thought that I couldn't get the prmtop and inpcrd files
 succesfully. Could you please help me to solve this problem and get prmtop
and inpcrd files succesfully with xleap ?

Thanks in advance.

sander -O –i min.in -o min.out -p n-dodecane.prmtop -c n-dodecane.inpcrd -r
n-dodecane.rst

1 antechamber -i n-dodecane.pdb -fi pdb -o n-dodecane_gin.gjf -fo gcrt

2 Run the gaussian ( #B3LYP/cc-pvTZ SCF=tight Test Pop=MK iop(6/33=2)
iop(6/42=6) opt )

3 antechamber -i n-dodecane_gin.out -fi gout -o c12.AA.mol2 -fo mol2 -nc 0
-c resp -at gaff -rn DEC

4 parmchk -i c12.AA.mol2 -f mol2 -o n-dodecane.frcmod ( generated empty
frcmod file )

5 antechamber -i c12.AA.mol2 -fi mol2 -o n-dodecane.gaff.pdb -fo pdb

6 use packmol with n-dodecane.gaff.pdb for getting 100 molecule ( added TER
cards ) n-dodecane.packmol100.pdb file

 Log file: ./leap.log

> #

> # ----- leaprc for loading the general Amber Force field.

> # This file is mostly for use with Antechamber

> #

> # load atom type hybridizations

> #

> addAtomTypes {

> { "h1" "H" "sp3" }

> { "h2" "H" "sp3" }

> { "h3" "H" "sp3" }

> { "h4" "H" "sp3" }

> { "h5" "H" "sp3" }

> { "ha" "H" "sp3" }

> { "hc" "H" "sp3" }

> { "hn" "H" "sp3" }

> { "ho" "H" "sp3" }

> { "hp" "H" "sp3" }

> { "hs" "H" "sp3" }

> { "hw" "H" "sp3" }

> { "hx" "H" "sp3" }

> { "o" "O" "sp2" }

> { "o2" "O" "sp2" }

> { "oh" "O" "sp3" }

> { "os" "O" "sp3" }

> { "ow" "O" "sp3" }

> { "c" "C" "sp2" }

> { "c1" "C" "sp2" }

> { "c2" "C" "sp2" }

> { "c3" "C" "sp3" }

> { "ca" "C" "sp2" }

> { "cc" "C" "sp2" }

> { "cd" "C" "sp2" }

> { "ce" "C" "sp2" }

> { "cf" "C" "sp2" }

> { "cg" "C" "sp2" }

> { "ch" "C" "sp2" }

> { "cp" "C" "sp2" }

> { "cq" "C" "sp2" }

> { "cu" "C" "sp2" }

> { "cv" "C" "sp2" }

> { "cx" "C" "sp2" }

> { "cy" "C" "sp2" }

> { "n" "N" "sp2" }

> { "n1" "N" "sp2" }

> { "n2" "N" "sp2" }

> { "n3" "N" "sp3" }

> { "n4" "N" "sp3" }

> { "na" "N" "sp2" }

> { "nb" "N" "sp2" }

> { "nc" "N" "sp2" }

> { "nd" "N" "sp2" }

> { "ne" "N" "sp2" }

> { "nf" "N" "sp2" }

> { "nh" "N" "sp2" }

> { "no" "N" "sp2" }

> { "s" "S" "sp2" }

> { "s2" "S" "sp2" }

> { "s3" "S" "sp3" }

> { "s4" "S" "sp3" }

> { "s6" "S" "sp3" }

> { "sh" "S" "sp3" }

> { "ss" "S" "sp3" }

> { "sx" "S" "sp3" }

> { "sy" "S" "sp3" }

> { "p2" "P" "sp2" }

> { "p3" "P" "sp3" }

> { "p4" "P" "sp3" }

> { "p5" "P" "sp3" }

> { "pb" "P" "sp3" }

> { "pd" "P" "sp3" }

> { "px" "P" "sp3" }

> { "py" "P" "sp3" }

> { "f" "F" "sp3" }

> { "cl" "Cl" "sp3" }

> { "br" "Br" "sp3" }

> { "i" "I" "sp3" }

> }

> #

> # Load the general force field parameter set.

> #

> gaff = loadamberparams gaff.dat

Loading parameters:
/home_palamut2/software/application/amber10/dat/leap/parm/gaff.dat

Reading title:

AMBER General Force Field for organic mol., add. info. at the end (June,
2003)

> HELP

Help is available on the following subjects:

_cmd_options_ _types_ add addAtomTypes

addIons addIons2 addPath addPdbAtomMap

addPdbResMap alias alignAxes bond

bondByDistance center charge check

clearPdbAtomMap clearPdbResMap clearVariables combine

copy createAtom createParmset createResidue

createUnit crossLink debugOff debugOn

debugStatus deleteBond deleteOffLibEntry deleteRestraint

desc deSelect displayPdbAtomMap displayPdbResMap

edit groupSelectedAtoms help impose

list listOff loadAmberParams loadAmberPrep

loadMol2 loadOff loadPdb loadPdbUsingSeq

logFile matchVariables measureGeom quit

remove restrainAngle restrainBond restrainTorsion

saveAmberParm saveAmberParmPert saveAmberParmPol
saveAmberParmPolPert

saveAmberPrep saveOff saveOffParm savePdb

scaleCharges select sequence set

setBox solvateBox solvateCap solvateDontClip

solvateOct solvateShell source transform

translate verbosity zMatrix

For a list of the current aliases, type "alias".

> DEC = loadMol2 c12.AA.mol2

Loading Mol2 file: ./c12.AA.mol2

Reading MOLECULE named DEC

> charge DEC

Total unperturbed charge: 0.000000

Total perturbed charge: 0.000000

> check DEC

Checking 'DEC'....

Checking parameters for unit 'DEC'.

Checking for bond parameters.

Checking for angle parameters.

Unit is OK.

> desc DEC

UNIT name: DEC

Head atom: null

Tail atom: null

Contents:

R<DEC 1>

> n-dodecane = loadpdb n-dodecane.packmol100.pdb

Loading PDB file: ./n-dodecane.packmol100.pdb

Enter zPdbReadScan from call depth 0.

Exit zPdbReadScan from call depth 0.

Matching PDB residue names to LEaP variables.

(Residue 0: DEC, Terminal/last, was not found in name map.)

(Residue 1: DEC, Terminal/last, was not found in name map.)

(Residue 2: DEC, Terminal/last, was not found in name map.)

(Residue 3: DEC, Terminal/last, was not found in name map.)

(Residue 4: DEC, Terminal/last, was not found in name map.)

(Residue 5: DEC, Terminal/last, was not found in name map.)

(Residue 6: DEC, Terminal/last, was not found in name map.)

(Residue 7: DEC, Terminal/last, was not found in name map.)

(Residue 8: DEC, Terminal/last, was not found in name map.)

(Residue 9: DEC, Terminal/last, was not found in name map.)

(Residue 10: DEC, Terminal/last, was not found in name map.)

(Residue 11: DEC, Terminal/last, was not found in name map.)

(Residue 12: DEC, Terminal/last, was not found in name map.)

(Residue 13: DEC, Terminal/last, was not found in name map.)

(Residue 14: DEC, Terminal/last, was not found in name map.)

(Residue 15: DEC, Terminal/last, was not found in name map.)

(Residue 16: DEC, Terminal/last, was not found in name map.)

(Residue 17: DEC, Terminal/last, was not found in name map.)

(Residue 18: DEC, Terminal/last, was not found in name map.)

(Residue 19: DEC, Terminal/last, was not found in name map.)

(Residue 20: DEC, Terminal/last, was not found in name map.)

(Residue 21: DEC, Terminal/last, was not found in name map.)

(Residue 22: DEC, Terminal/last, was not found in name map.)

(Residue 23: DEC, Terminal/last, was not found in name map.)

(Residue 24: DEC, Terminal/last, was not found in name map.)

(Residue 25: DEC, Terminal/last, was not found in name map.)

(Residue 26: DEC, Terminal/last, was not found in name map.)

(Residue 27: DEC, Terminal/last, was not found in name map.)

(Residue 28: DEC, Terminal/last, was not found in name map.)

(Residue 29: DEC, Terminal/last, was not found in name map.)

(Residue 30: DEC, Terminal/last, was not found in name map.)

(Residue 31: DEC, Terminal/last, was not found in name map.)

(Residue 32: DEC, Terminal/last, was not found in name map.)

(Residue 33: DEC, Terminal/last, was not found in name map.)

(Residue 34: DEC, Terminal/last, was not found in name map.)

(Residue 35: DEC, Terminal/last, was not found in name map.)

(Residue 36: DEC, Terminal/last, was not found in name map.)

(Residue 37: DEC, Terminal/last, was not found in name map.)

(Residue 38: DEC, Terminal/last, was not found in name map.)

(Residue 39: DEC, Terminal/last, was not found in name map.)

(Residue 40: DEC, Terminal/last, was not found in name map.)

(Residue 41: DEC, Terminal/last, was not found in name map.)

(Residue 42: DEC, Terminal/last, was not found in name map.)

(Residue 43: DEC, Terminal/last, was not found in name map.)

(Residue 44: DEC, Terminal/last, was not found in name map.)

(Residue 45: DEC, Terminal/last, was not found in name map.)

(Residue 46: DEC, Terminal/last, was not found in name map.)

(Residue 47: DEC, Terminal/last, was not found in name map.)

(Residue 48: DEC, Terminal/last, was not found in name map.)

(Residue 49: DEC, Terminal/last, was not found in name map.)

(Residue 50: DEC, Terminal/last, was not found in name map.)

(Residue 51: DEC, Terminal/last, was not found in name map.)

(Residue 52: DEC, Terminal/last, was not found in name map.)

(Residue 53: DEC, Terminal/last, was not found in name map.)

(Residue 54: DEC, Terminal/last, was not found in name map.)

(Residue 55: DEC, Terminal/last, was not found in name map.)

(Residue 56: DEC, Terminal/last, was not found in name map.)

(Residue 57: DEC, Terminal/last, was not found in name map.)

(Residue 58: DEC, Terminal/last, was not found in name map.)

(Residue 59: DEC, Terminal/last, was not found in name map.)

(Residue 60: DEC, Terminal/last, was not found in name map.)

(Residue 61: DEC, Terminal/last, was not found in name map.)

(Residue 62: DEC, Terminal/last, was not found in name map.)

(Residue 63: DEC, Terminal/last, was not found in name map.)

(Residue 64: DEC, Terminal/last, was not found in name map.)

(Residue 65: DEC, Terminal/last, was not found in name map.)

(Residue 66: DEC, Terminal/last, was not found in name map.)

(Residue 67: DEC, Terminal/last, was not found in name map.)

(Residue 68: DEC, Terminal/last, was not found in name map.)

(Residue 69: DEC, Terminal/last, was not found in name map.)

(Residue 70: DEC, Terminal/last, was not found in name map.)

(Residue 71: DEC, Terminal/last, was not found in name map.)

(Residue 72: DEC, Terminal/last, was not found in name map.)

(Residue 73: DEC, Terminal/last, was not found in name map.)

(Residue 74: DEC, Terminal/last, was not found in name map.)

(Residue 75: DEC, Terminal/last, was not found in name map.)

(Residue 76: DEC, Terminal/last, was not found in name map.)

(Residue 77: DEC, Terminal/last, was not found in name map.)

(Residue 78: DEC, Terminal/last, was not found in name map.)

(Residue 79: DEC, Terminal/last, was not found in name map.)

(Residue 80: DEC, Terminal/last, was not found in name map.)

(Residue 81: DEC, Terminal/last, was not found in name map.)

(Residue 82: DEC, Terminal/last, was not found in name map.)

(Residue 83: DEC, Terminal/last, was not found in name map.)

(Residue 84: DEC, Terminal/last, was not found in name map.)

(Residue 85: DEC, Terminal/last, was not found in name map.)

(Residue 86: DEC, Terminal/last, was not found in name map.)

(Residue 87: DEC, Terminal/last, was not found in name map.)

(Residue 88: DEC, Terminal/last, was not found in name map.)

(Residue 89: DEC, Terminal/last, was not found in name map.)

(Residue 90: DEC, Terminal/last, was not found in name map.)

(Residue 91: DEC, Terminal/last, was not found in name map.)

(Residue 92: DEC, Terminal/last, was not found in name map.)

(Residue 93: DEC, Terminal/last, was not found in name map.)

(Residue 94: DEC, Terminal/last, was not found in name map.)

(Residue 95: DEC, Terminal/last, was not found in name map.)

(Residue 96: DEC, Terminal/last, was not found in name map.)

(Residue 97: DEC, Terminal/last, was not found in name map.)

(Residue 98: DEC, Terminal/last, was not found in name map.)

(Residue 99: DEC, Terminal/last, was not found in name map.)

  total atoms in file: 3800

> saveAmberParm n-dodecane n-dodecane.prmtop n-dodecane.inpcrd

Checking Unit.

Building topology.

Building atom parameters.

Building bond parameters.

Building angle parameters.

Building proper torsion parameters.

Building improper torsion parameters.

 total 0 improper torsions applied

Building H-Bond parameters.

Not Marking per-residue atom chain types.

Marking per-residue atom chain types.

  (Residues lacking connect0/connect1 -

   these don't have chain types marked:

      res total affected

      DEC 100

  )

 (no restraints)

> savepdb n-dodecane n-dodecane.leap.pdb

Writing pdb file: n-dodecane.leap.pdb

> QUIT Quit

2009/1/26 M. L. Dodson <activesitedynamics_at_comcast.net>

> oguz gurbulak wrote:
>
>> Dear D Case,
>>
>> I again run some experiments according to your advices and my
>> min.out file is like in below. I used packmol, I wrote box size for
>> x, y, z : 9.825 A and created a packmol pdb file for this system. So
>> I didn't use solvatebox command in xleap. I thought that there is a
>> problem about using packmol. If so, How can I solve this problem and
>> use packmol without any errors ? In this sense, I'm waiting for your
>> help and also other people's help who have enough experience on
>> PACKMOL package. Or I'm waiting for some alternative solutions of
>> you related with LEAP.
>>
>> Sincerely,
>>
>> -------------------------------------------------------
>> Amber 10 SANDER 2008
>> -------------------------------------------------------
>>
>> | PMEMD implementation of SANDER, Release 10
>>
>> | Run on 01/26/2009 at 15:55:22
>>
>> [-O]verwriting output
>>
>> File Assignments:
>> | MDIN: /home_palamut2/ogurbulak/c7AMBER10/min/min.in
>> | MDOUT: /home_palamut2/ogurbulak/c7AMBER10/min/min.out
>> | INPCRD: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.inpcrd
>> | PARM: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.prmtop
>> | RESTRT:
>> /home_palamut2/ogurbulak/c7AMBER10/min/n-dodecane.rst |
>> REFC: refc
>> | MDVEL: mdvel
>> | MDEN: mden
>> | MDCRD: mdcrd
>> | MDINFO: mdinfo
>> |LOGFILE: logfile
>>
>> Here is the input file:
>> initial minimization
>> &cntrl
>> imin=1,
>> maxcyc=500,
>> ncyc=250,
>> ntb=1,
>> cut=9.825,
>> ntpr=100,
>> ntc=2, ntf=2,
>> /
>>
>> | ERROR: Box parameters not found in inpcrd
>> file!
>>
>>
> Sorry to break into this thread, but I think there is a problem with
> packmol-generated pdb files. The individual molecules need a TER card
> between them, and packmol leaves the TER cards out. There was a
> script posted to the email list to insert them automatically, but I
> can't find the copy I made from the email.
>
> If this causes anyone to remember, please repost the script.
>
> Did leap finish without errors? Did it complain about the lack of
> TER records?
>
> By the way, it would be a help if you used gzip or some standard
> compression program to compress files posted to the list. Some of us
> do not have a program to handle these rar files. What are they? It
> is identified by file(1) as "inpcrd.rar: RAR archive data, v14, os: Win32"
>
> Bud Dodson
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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