AMBER Archive (2006)

Subject: AMBER: Problem with restarting MD simulation

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Tue Aug 08 2006 - 00:02:56 CDT

Dear amber users,
                         I am not able to restart my MD simulations. sander
is giving the following error:

Unit 30 Error on OPEN: l42b18_eqm1.rst

The rst file is attached and output file is :

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

Amber 9 SANDER 2006

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

| Run on 08/06/2006 at 11:25:51

[-O]verwriting output

File Assignments:

| MDIN: md_eqm.in

| MDOUT: md_eqm1.out

|INPCRD: l42b18_eqm1.rst

| PARM: l42b18.prmtop

|RESTRT: l42b18_eqb2.rst

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

Here is the input file:

Eqm md simulation of L42B18 dna in saltconc 5mM

&cntrl

imin=0,

irest=1,

ntwr=100,

ntx=5,

ntpr=100,

ntwx=1000,

nstlim=50000,

dt=0.001,

cut=12,

ntb=0,

igb=1,saltcon=0.05,

ntt=3, gamma_ln=1.0,

tempi=300,

temp0=305,

/

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

1. RESOURCE USE:

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

| Flags:

| New format PARM file being parsed.

| Version = 1.000 Date = 08/01/06 Time = 03:12:54

NATOM = 2662 NTYPES = 15 NBONH = 946 MBONA = 1924

NTHETH = 2242 MTHETA = 2966 NPHIH = 4770 MPHIA = 5222

NHPARM = 0 NPARM = 0 NNB = 14824 NRES = 84

NBONA = 1924 NTHETA = 2966 NPHIA = 5222 NUMBND = 37

NUMANG = 76 NPTRA = 42 NATYP = 25 NPHB = 0

IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0

NCOPY = 0

Implicit solvent radii are modified Bondi radii (mbondi)

| Memory Use Allocated

| Real 139379

| Hollerith 16058

| Integer 159145

| Max Pairs 1

| nblistReal 0

| nblist Int 0

| Total 1773 kbytes

| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

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

2. CONTROL DATA FOR THE RUN

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

General flags:

imin = 0, nmropt = 0

Nature and format of input:

ntx = 5, irest = 1, ntrx = 1

Nature and format of output:

ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 100

iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0

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

Potential function:

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

ipol = 0, gbsa = 0, iesp = 0

dielc = 1.00000, cut = 12.00000, intdiel = 1.00000

saltcon = 0.05000, offset = 0.09000, gbalpha= 1.00000

gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500

rdt = 0.00000, rgbmax = 25.00000

alpb = 0

scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:

ibelly = 0, ntr = 0

Molecular dynamics:

nstlim = 50000, nscm = 1000, nrespa = 1

t = 0.00000, dt = 0.00100, vlimit = 20.00000

Langevin dynamics temperature regulation:

ig = 71277

temp0 = 305.00000, tempi = 300.00000, gamma_ln= 1.00000

Unit 30 Error on OPEN: l42b18_eqm1.rst

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

Please help...
thanx in advance... 

-- 
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,
----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu