AMBER Archive (2008)

Subject: AMBER: Problems with sleap and amoeba

From: Neil J. Henson (neil.henson_at_lanl.gov)
Date: Tue Aug 19 2008 - 18:16:17 CDT

We are running :
Amber 10
AmberTools 1.2
Fedora 9 x86_64
gcc 4.3.0, pgf90 7.2-3

We are trying to use sleap with the amoeba force field to build input
files for a single metal cation (La3+) with a single water molecule. We
have been running similar systems with tinker, but want to switch to Amber
to exploit the parallellism. We modified the amoeba.prm file to include
parameters for La :

# Arbitrary lanthanum potential parameters added for now

atom 202 39 O "AMOEBA Water O" 8 15.995 2
atom 203 40 H "AMOEBA Water H" 1 1.008 1
atom 204 41 La "Lanthanide Ion La3+" 57 138.900 12

vdw 39 3.405 0.1100
vdw 40 2.655 0.0135 0.910
vdw 41 2.455 0.3213

bond 39 40 529.6 0.9572
angle 40 39 40 34.05 108.50
ureybrad 40 39 40 38.25 1.5537

polarize 202 0.837 203
polarize 203 0.496 202
polarize 204 0.120

multipole 202 203 -203 -0.51966
                                       0.00000 0.00000 0.14279
                                       0.37928
                                       0.00000 -0.41809
                                       0.00000 0.00000 0.03881
multipole 203 202 203 0.25983
                                      -0.03859 0.00000 -0.05818
                                      -0.03673
                                       0.00000 -0.10739
                                      -0.00203 0.00000 0.14412

multipole 204 0 0 1.00000
                                       0.00000 0.00000 0.00000
                                       0.00000
                                       0.00000 0.00000
                                       0.00000 0.00000 0.00000

and created a La.lib file to create a residue LAN for the cation :

!!index array str
 "LAN"
!entry.LAN.unit.atoms table str name str type int typex int resx int
flags int seq int
 elmnt dbl chg
 "La1" "204" 0 1 17825795 1 57 3.000000
!entry.LAN.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "La1" "204" 0 -1 0.0
!entry.LAN.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.LAN.unit.childsequence single int
 2
!entry.LAN.unit.connect array int
 0
 0
!entry.LAN.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
!entry.LAN.unit.name single str
 "LAN"
!entry.LAN.unit.positions table dbl x dbl y dbl z
    0.000000 0.000000 0.000000
!entry.LAN.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 0 0 0 0 0 0
!entry.LAN.unit.residues table str name int seq int childseq int
startatomx str restype
 int imagingx
 "LAN" 1 2 1 "p" 0
!entry.LAN.unit.residuesPdbSequenceNumber array int
 0
!entry.LAN.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.LAN.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0

Our pdb file is :

ATOM 1 La1 LAN 1 -0.127 0.025 1.772
ATOM 2 O WAT 2 -1.237 -0.681 4.125
ATOM 3 H1 WAT 2 -0.974 -1.561 4.484
ATOM 4 H2 WAT 2 -2.091 -0.476 4.518
END

Our leaprc is a modified leaprc.amoeba with the following at the beginning :

% head leaprc.amoebapro-lan
set default echo on
loadoff amoeba_amino.off
loadoff amoeba_aminont.off
loadoff amoeba_aminoct.off
loadoff amoeba_wat.off

loadamoebaparams amoeba-lan.prm

addPdbResMap {
  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }

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

Here is what we saw :

% sleap
[gtkleap]$ source leaprc.amoebapro-lan

[.....]
read amoeba mploe
read amoeba atom
read amoeba atom
read amoeba atom
read amoeba vdw
read amoeba vdw
read amoeba vdw
read amoeba bond
read amoeba angl
read amoeba ureybrad
read amoeba polar
read amoeba polar
read amoeba polar
read amoeba mploe
read amoeba mploe
read amoeba mploe

[gtkleap]$ set default fastbld on
[gtkleap]$ loadoff LAN.lib
[gtkleap]$ xxx = loadpdb La-H2O.pdb
sleap: pertab.cpp:169: static const char*
mort::pertab_t::get_symbol(size_t): Assertion `element != 0' failed.
Aborted

I am thinking that the error indicates that it doesn't like my 'La'
element name, but I defined it in both the prm file and a LAN.lib file.
What am I missing here?

Thanks,
Neil. 

---
Neil Henson
T-12, Los Alamos National Laboratory
Correspondence or TSPA

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