AMBER Archive (2006)

Subject: Fwd: Fwd: AMBER: MMPBSA error

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Wed Jun 14 2006 - 06:27:51 CDT

Dear *Heike*

I have already done this by using 'ambpdb' with complex and I found the
error (see below). So, how I solve this problem ? By the way, I do ambpdb
with ligand and enzyme separately and the result is ok. Therefore, I
think it must be some errors in complex file (complex trajectorie and
complex topology file). I thinks I do with mmpbsa for couple weeks. Please
help me again.

Thanks

Jitrayut

[jitrayut_at_localhost 01_GenerateSnapshots]$ ambpdb -p md_com.top
<enz_pep_pH7_com.crd.1> check_com.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 06/14/06 Time = 08:10:02

  ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 27939 3444
COULD NOT READ COORDINATES FROM RESTRT FILE

---------- Forwarded message ----------
From: Heike.Meiselbach_at_chemie.uni-erlangen.de <
Heike.Meiselbach_at_chemie.uni-erlangen.de>
Date: 14 มิ.ย. 2006, 15:50 น.
Subject: Re: Fwd: AMBER: MMPBSA error
To: jitrayut jitonnom <jitrayut.018_at_gmail.com>

Hi,

in your sander output is the information about your problem.

FATAL: NATOM mismatch in coord and topology files

Your coord and topology file, that you used, is not correct. You can check
this, by creating a PDB-file with "ambpdb". Create a PDB with the topology
that you used in the mm_pbsa.in, in your case "dock71.top", and the coord
file, in your case "enz_pep_pH7_com.crd.1". Than, check the PDB-file. Is
the atom number correct or not. And/Or load the pdb in rasmol or VMD or
~E. - is the structure OK, or not? Does "ambpdb" not create a PDB-file and
give a mistake message, than your input file for generate snapshot is not
correct. Then check the following points:
BOX:
NTOTAL:
NUMBER_LIG_GROUPS:
LSTART:
LSTOP:
NUMBER_REC_GROUPS:
RSTART:
RSTOP:

Good look

Heike
> Dear *Heike*
> I don't understand what do you mean "Is the pdb-File correct? " Did you
> mean
> the format pdb file? or you maybe mean the number atoms in pdb is correct
> according to the mmpbsa script. Please give me some more details.
>
> Thanks in advance for your help
>
> Best regards
>
> Jitrayut
>
>
> ---------- Forwarded message ----------
> From: Heike.Meiselbach_at_chemie.uni-erlangen.de <
> Heike.Meiselbach_at_chemie.uni-erlangen.de>
> Date: 13 ÁÔ.Â. 2006, 22:27 ¹.
> Subject: Re: AMBER: MMPBSA error
> To: amber_at_scripps.edu
>
> Hi,
>
> check your structure with:
> ambpdb -p ../dock71.top < ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1 >
> check_Complex.pdb
>
> Is the pdb-File correct? If this is not the case, look in your generate
> snapshot input file: If your simulation was carried out in water, you must
> set the box information to yes. NTOTAL, the number of all atoms (with
> water end counterions).
> You must create a topology file from your complex without water and
> counterions.
>
> good luck,
> Heike
>
>
>
>
>
>> Dear amber users
>>
>> This is errors from mmpbsa. I generate three parameters files of LIG,REC
>> and
>> COM. My mdcrd file is an explicit md including water. To do the mmpbsa,
>> I
>> generate the snapshots from this parameters files for the first step but
>> the
>> second step that all trajectories were calculated, I found errors which
>> show
>> below. So, I don't understand where this errors happend.
>>
>> Please help me for this problems.
>>
>> Thanks
>>
>> Jitrayut
>>
>>
>>
>> [jitrayut_at_localhost 02_MMPBSA_Stability]$
>> /AMBER/amber9/exe/sander
>> -O -i sander_com.in -o sander_com.1.out -c
>> ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1 -p ../dock71.top not
>> successful
>> [2]- Exit 25 mm_pbsa.pl mm_pbsa.in >mm_pbsa.log
>>
>>
>>
>>
>> -------------------------------------------------------
>> Amber 9 SANDER 2006
>> -------------------------------------------------------
>>
>> | Run on 06/10/2006 at 18:27:42
>> [-O]verwriting output
>>
>> File Assignments:
>> | MDIN: sander_com.in
>> | MDOUT: sander_com.1.out
>> |INPCRD: ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1
>> | PARM: ../dock71.top
>> |RESTRT: restrt
>> | REFC: refc
>> | MDVEL: mdvel
>> | MDEN: mden
>> | MDCRD: mdcrd
>> |MDINFO: mdinfo
>> |INPDIP: inpdip
>> |RSTDIP: rstdip
>>
>>
>> Here is the input file:
>>
>> File generated by mm_pbsa.pl. Using MM GB
>>
>> cntrl
>> ntf = 1, ntb = 0, dielc = 1.0,
>> idecomp= 0,
>> igb = 2, saltcon= 0.00,
>> offset = 0.09,
>> intdiel= 1.0, extdiel= 80.0,
>> gbsa = 0, surften= 1.0,
>> cut = 999.0, nsnb = 99999,
>> scnb = 2.0, scee = 1.2,
>>
>> imin = 1, maxcyc = 1, ncyc = 0,
>> &end
>>
>>
>
--------------------------------------------------------------------------------
>> 1. RESOURCE USE:
>>
>
--------------------------------------------------------------------------------
>>
>> | Flags:
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 05/28/06 Time = 19:45:26
>> NATOM = 27939 NTYPES = 16 NBONH = 26195 MBONA = 1781
>> NTHETH = 3825 MTHETA = 2437 NPHIH = 7403 MPHIA = 4752
>> NHPARM = NPARM = NNB = 51578 NRES = 8402
>> NBONA = 1781 NTHETA = 2437 NPHIA = 4752 NUMBND = 46
>> NUMANG = 92 NPTRA = 42 NATYP = 31 NPHB = 1
>> IFBOX = 1 NMXRS = 25 IFCAP = NEXTRA = 0
>> NCOPY = 0
>>
>> Implicit solvent radii are modified Bondi radii (mbondi)
>>
>> | Memory Use Allocated
>> | Real 1788610
>> | Hollerith 176038
>> | Integer 617374
>> | Max Pairs 1
>> | nblistReal 0
>> | nblist Int 0
>> | Total 17072 kbytes
>> | Duplicated dihedrals
>> | Duplicated dihedrals
>>
>> BOX TYPE: RECTILINEAR
>>
>>
>>
>> 2. CONTROL DATA FOR THE RUN
>>
>
--------------------------------------------------------------------------------
>>
>> General flags:
>> imin = 1, nmropt = 0
>>
>> Nature and format of input:
>> ntx = 1, irest = 0, ntrx = 1
>>
>> Nature and format of output:
>> ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
>> 500
>> iwrap = 0, ntwx = 0, ntwv = 0, ntwe
>> = 0
>> ioutfm = 0, ntwprt = 0, idecomp = 0,
>> rbornstat= 0
>>
>> Potential function:
>> ntf = 1, ntb = 0, igb = 2, nsnb =
>> 99999
>> ipol = 0, gbsa = 0, iesp = 0
>> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
>> saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000
>> gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000
>> rdt = 0.00000, rgbmax = 25.00000
>> alpb = 0
>> scnb = 2.00000, scee = 1.20000
>>
>> Frozen or restrained atoms:
>> ibelly = 0, ntr = 0
>>
>> Energy minimization:
>> maxcyc = 1, ncyc = 0, ntmin = 1
>> dx0 = 0.01000, drms = 0.00010
>> Setting ifbox to 3 for non-orthogonal unit cell
>> | INFO: Old style inpcrd file read
>>
>>
>>
>
--------------------------------------------------------------------------------
>> 3. ATOMIC COORDINATES AND VELOCITIES
>>
>
--------------------------------------------------------------------------------
>>
>>
>> FATAL: NATOM mismatch in coord and topology files
>>
>
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