[AMBER] about Nmod in amber11

From: juan zeng <azengjuan.gmail.com>
Date: Wed, 9 Mar 2011 15:25:11 +0800

Dear Amber Users:
                      When I calculated the entropy with mm_pbsa.pl in
amber11,I get this errors in nmod_com.1.out file:


Root-mean-square gradient of input coords is 0.388121768343034

This is greater than the requested maximum: 1.000000000000000E-003
But in my sanmin_com.1.out fileŁ¬this RMS value is 9.5896E-05 and is smaller
than 1.000000000000000E-003. Can you give me some ideas what happened.I will
appreciate you very much.the nmod_com.1.out and sanmin_com.1.out file were
upload with attachment and my input file is as this:

.GENERAL
VERBOSE 0
PARALLEL 0
PREFIX snapshot
PATH ../snapshot/
START 1
STOP 10
OFFSET 1
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./chainA_com_resp_gas.prmtop
RECPT ./chainA_pro_resp_gas.prmtop
LIGPT ./chainA_lig_resp_gas.prmtop
GC 0
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 1

.NM
PROC 2
MAXCYC 50000
DRMS 0.0001
IGB 0
SALTCON 0.00
EXTDIEL 80.0
SURFTEN 0.0072
DIELC 4
.PROGRAMS


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Received on Tue Mar 08 2011 - 23:30:03 PST
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