[CPMD-list] total atom numbers in QM/MM calc

[Philip Shemella]

Hi All,

I am setting up a solvated protein system for QM/MM (CPMD/Gromos).  From 
this part of the manual:
http://www.cpmd.org/manual/node114.html
I am using hydrogen capping, so I setting up the initial run with ADD_H 
in order to get the CRD_FIN.grm file with capping H atoms.

The stoppage comes from mm_detit.f (line 145).  I've looked into the 
code, and found that the last 3 integers printed are NATq (# quantum 
atoms), NATm (# total atoms), and NRTOT (# protein NRPT + # solvent NSOLV).

*mm_detit.f*
     138        DO is=NSPq+1,NSPm
     139          NATm=NATm+NAm(is)
     140        ENDDO
     141        NATm=NATm+NATq
     142
     143        if (NATm.ne.NRTOT) then
     144          write(6,*)NATq,NATm,NRTOT
     145          CALL STOPGM('mm_detit','error defining NATm')
     146        endif

In my case, each water molecule is treat as part of the protein, so 
NSOLV=0 and NRPT = 6314.  NRTOT = 6314 + 10 capping H atoms = 6324 which 
the code recognizes.

I don't understand the loop at line 138 of mm_detit.f, shown below.


Somehow the NATm is ending up as 6325.  My TOP and CRD files all show 
6314 atoms.

One idea I have is that two QM atoms have two capping H atoms.  Perhaps 
this will be another problem down the road, but I don't see how that 
would generate the current error.
Any suggestions for where this extra atom is coming from would be 
greatly appreciated.  I can send the TOP, INP, and CRD files if 
necessary.  Below are part of the output, and the input.  Also, I am 
using  VERSION 3.11.1 with the recent update to mm_get_NSX.

Many thanks, Phil Shemella


==================================
*Middle and tail of output*
==================================
  NRP    =        6314    NPM =     1
  NRPT   = NRP*NPM =        6314
  NRAM   =     1    NSM =           0
  NSOLV  = NRAM*NSM =           0
  NATTOT = NRPT + NSOLV =        6314
....
...
..
.
CAPPING  DANGLING BOND BETWEEN:    73    63
CAPPING  DANGLING BOND BETWEEN:    79    82
CAPPING  DANGLING BOND BETWEEN:   110   112
CAPPING  DANGLING BOND BETWEEN:   110   125
CAPPING  DANGLING BOND BETWEEN:  1149  1147
CAPPING  DANGLING BOND BETWEEN:  1189  1187
CAPPING  DANGLING BOND BETWEEN:  1994  1991
CAPPING  DANGLING BOND BETWEEN:  2243  2231
CAPPING  DANGLING BOND BETWEEN:  2289  2291
CAPPING  DANGLING BOND BETWEEN:  2289  2296

    QUANTUM SYSTEM:
    NAX:          61
    NSX:           6
    FULL SYSTEM:
    NAX:          61
    NSX:         117
          136        6325        6324


  PROGRAM STOPS IN SUBROUTINE mm_detit| error defining NATm



==================================
*INPUT*
==================================
&CPMD
  QMMM
  MOLECULAR DYNAMICS CLASSICAL
  MAXSTEP
  10
  MIRROR
&END

&ATOMS
*C_VDB_BLYP.psp NEWF FORMATTED
    LMAX=P
    31
    73 77 79 95 99 101 106 110 1149 1151 1189 1192
    1194 1198 1191 1994 2243 2247 2249 2252 2255 2258
    2260 2264 2266 2269 2274 2278 2280 2285 2289

*N_VDB_BLYP.psp NEWF FORMATTED
    LMAX=P
    12
    75 97 108 1193 1196 2245 2253 2257 2262 2271 2276 2287

*O_VDB_BLYP.psp NEWF FORMATTED
    LMAX=P
    20
    74 96 107 1155 1995 1996 2244 2261 2270 2275 2286
    2391 3510 4170 4263 4350 4401 4416 6051 6183

*S_VDB_BLYP.psp NEWF FORMATTED
    LMAX=P
    2
    104 2283

*H_VDB_BLYP.psp NEWF FORMATTED
    LMAX=S
    61
    76 78 80 81 98 100 102 103 105 109 111 1150 1152
    1153 1154 1156 1190 1191 1195 1197 1199 1992 1993
    2246 2248 2250 2251 2254 2256 2259 2263 2265 2267
    2268 2272 2273 2277 2279 2281 2282 2284 2288 2290
    2392 2393 3511 3512 4171 4172 4264 4265 4351 4352
    4402 4403 4417 4418 6052 6053 6184 6185

*H_VDB_BLYP.psp NEWF FORMATTED ADD_H
    LMAX=S
    10

&END

&SYSTEM
   POISSON SOLVER TUCKERMAN
   SYMMETRY
   0
   CELL
   30.0  1.0  1.0  0  0  0
   CUTOFF
   10.0
   CHARGE
   -1.0
&END

&DFT
   NEWCODE
   FUNCTIONAL BLYP
&END

&QMMM
   AMBER
   CAPPING
   TOPOLOGY
    gromos.top
   COORDINATES
    gromos.crd
   INPUT
    gromos.inp

  ARRAYSIZES

  MAXATT 27
  MAXAA2 1482
  MAXNRP 6324
  MAXNBT 56
  MAXBNH 5155
  MAXBON 1203
  MAXTTY 105
  MXQHEH 2686
  MAXTH  1633
  MAXQTY 10
  MAXHIH 10
  MAXQHI 10
  MAXPTY 43
  MXPHIH 4798
  MAXPHI 2856
  MAXCAG 2074
  MAXAEX 30637
  MXEX14 6196

  END ARRAYSIZES

&END
========================================