AMBER Archive (2005)

Subject: AMBER: problem with protein minimization

From: yen li (chem_me2000_at_yahoo.com)
Date: Mon Feb 21 2005 - 03:12:02 CST

Dear amber people,
I am trying to perform a simple vaccum minimization of
a stratight chain of protein having 160 amino acids
(all the main chain dihedrals are 180 degrees, except
for proline). with the same sequence of the native
folded protein, i am able to run the minimization with
amber7, but with the straight chain, it gives error
for some of the parameters of sizes.h header file. The
output file is given below. I also tried changing the
indicated parameters and then recompiling, but it
didnt help. I could not understand the reason for such
a difference in behavoiur. Some help in this regard
will be appreciated.
thanks
  

-------------------------------------------------------

Amber 7 SANDER Scripps/UCSF 2002

-------------------------------------------------------

| Sun Feb 20 22:56:33 2005

[-O]verwriting output

File Assignments:

| MDIN: p1.in

| MDOUT: 119l.npNa.out

|INPCRD: 119l.npNn.crd

| PARM: 119l.npN.top

|RESTRT: 119l.npNa.crd

| REFC: 119l.npNn.crd

| MDVEL: mdvel

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

 

Here is the input file:

&cntrl

imin = 1, maxcyc = 500, ncyc=150, ntmin=1,

cut = 9.0,ntb=0,ntwr=10,

ntpr = 10,

ibelly = 1,

&end

&ewald

use_pme=0

&end

-- group input:select only water to be mobile--

FIND

* H * *

* HC * *

* HO * *

* HS * *

* HA * *

* H1 * *

SEARCH

RES 1 99999

END

FIND

* H2 * *

* H3 * *

* H4 * *

* H5 * *

* HP * *

* * * WAT

* * * Cl-

SEARCH

RES 1 99999

END

END

--------------------------------------------------------------------------------

1. RESOURCE USE:

--------------------------------------------------------------------------------

| Flags:

| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic
simulation

| INFO: Old style PARM file read

NATOM = 2613 NTYPES = 14 NBONH = 1319 MBONA = 1314

NTHETH = 2983 MTHETA = 1770 NPHIH = 5570 MPHIA = 3269

NHPARM = 0 NPARM = 0 NNB = 14365 NRES = 162

NBONA = 1314 NTHETA = 1770 NPHIA = 3269 NUMBND = 41

NUMANG = 88 NPTRA = 39 NATYP = 27 NPHB = 0

IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0

 

| Memory Use Allocated Used

| Real 10000000 206546

| Hollerith 1000000 15842

| Integer 40000000 36195372

| Max Nonbonded Pairs:10000000

| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------

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 = 10, ntrx = 1, ntwr = 10

iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0

ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:

ntf = 1, ntb = 0, igb = 0, nsnb = 25

ipol = 0, gbsa = 0

dielc = 1.00000, cut = 9.00000, intdiel = 1.00000

scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:

ibelly = 1, ntr = 0

Energy minimization:

maxcyc = 500, ncyc = 150, ntmin = 1

dx0 = 0.01000, dxm = 0.50000, drms = 0.00010

Warning: Although EWALD will work with belly

(for equilibration), it is not strictly correct!

 

LOADING THE BELLY ATOMS AS GROUPS

----- READING GROUP 1; TITLE:

-- group input:select only water to be mobile--

ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS
WILL BE INCLUDED IN GROUP BELOW

GRAPH NAME = * SYMBOL = H TREE SYMBOL = * RESIDUE TYPE
= *

GRAPH NAME = * SYMBOL = HC TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = HO TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = HS TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = HA TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = H1 TREE SYMBOL = * RESIDUE
TYPE = *

GRP 1 RES 1 TO 162

Number of atoms in this group = 1287

----- READING GROUP 2; TITLE:

ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS
WILL BE INCLUDED IN GROUP BELOW

GRAPH NAME = * SYMBOL = H2 TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = H3 TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = H4 TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = H5 TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = HP TREE SYMBOL = * RESIDUE
TYPE = *

GRAPH NAME = * SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= WAT

GRAPH NAME = * SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= Cl-

GRP 2 RES 1 TO 162

Number of atoms in this group = 32

----- END OF GROUP READ -----

--------------------------------------------------------------------------------

3. ATOMIC COORDINATES AND VELOCITIES

--------------------------------------------------------------------------------

begin time read from input coords = 0.000 ps

Number of triangulated 3-point waters found: 0

Sum of charges from parm topology file = 7.99999993

Assuming uniform neutralizing plasma

--------------------------------------------------------------------------------

4. RESULTS

--------------------------------------------------------------------------------

---------------------------------------------------

eedmeth=4: Setting switch to one everywhere

---------------------------------------------------

Exceeding lastist in get_istack

lastist = 30000000

top_stk= 21868392

isize = 21027300

request= 42895692

Increase MAX_ISTACK in sizes.h and recompile

                
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