[gmx-users] Methanol SOL :Number of solvent molecules = 0
sharada
sharada at ccmb.res.in
Tue Dec 11 06:29:12 CET 2007
Dear Dr. Justin A. Lemkul
Thank you for your reply. I tried adding the line 'SOL 522 ' at the end of the .top file
but genbox is deleting the line.
------------------------------------------------------------
Output configuration contains 1076 atoms in 341 residues
Volume : 24.1334 (nm^3)
Density : 720.413 (g/l)
Number of SOL molecules: 0
Processing topology
Removing line #480 'SOL 522' from topology file (agg2.top)
-------------------------------------------------------------------------------------------
Thankyou Dr. Xavier Periole for indicating that the bonds and angle information does not match with the original Gromos distributed file. I am inserting methanol.itp file which came with gromacs distribution. I downloaded the methanol216.gro.gz from gromacs site. Should I change the bond values in the itp file? But it still does not solve the problem of 'SOL molecules'. Since .top file indicates "#include "spc.itp". So if I change it to #methanol.itp" it should work.
-----------------------------------------------
[root at ccmb top]# more methanol.itp
#ifndef _FF_GROMOS96
[ atomtypes ]
; type mass charge ptype c6 c12
OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6
OW 15.999 -0.82 A 2.6170e-3 2.6330e-6
CMET 15.035 0.29 A 8.8758e-3 17.8426e-6
H 1.008 0.4 A 0.0 0.0
HW 1.008 0.41 A 0.0 0.0
#endif
[ moleculetype ]
; name nrexcl
Methanol 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
#ifdef _FF_GROMOS96
1 CMET 1 MeOH Me1 1 0.176 15.035
2 OMET 1 MeOH O2 1 -0.574 15.999
3 H 1 MeOH H3 1 0.398 1.008
#else
1 CMET 1 MeOH Me1 1 Regards
sharada 0.29 15.035
2 OMET 1 MeOH O2 1 -0.69 15.999
3 H 1 MeOH H3 1 0.40 1.008
#endif
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.13600 376560.
2 3 1 0.10000 313800.
[ angles ]
; ai aj ak funct c0 c1
1 2 3 1 108.53 397.5
Regards
sharada
(CCMB)
-------------------------------------------------------------------------------------------------------------------------------------------------
-- Original Message --
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 10 Dec 2007 06:36:56 -0500
Subject: Re: [gmx-users] Methanol SOL :Number of solvent molecules = 0
Quoting sharada <sharada at ccmb.res.in>:
> 526MeOH Me1 1629 2.760 3.368 2.738
> 526MeOH O2 1630 2.695 3.423 2.632
> 526MeOH H3 1631 2.615 3.371 2.606
> 527MeOH Me1 1632 0.288 3.224 2.925
> 527MeOH O2 1633 0.194 3.156 2.996
> 527MeOH H3 1634 0.212 3.059 2.983
> 528MeOH Me1 1635 2.506 3.095 2.599
> 528MeOH O2 1636 2.457 3.218 2.567
> 528MeOH H3 1637 2.390 3.204 2.494
> 3.30500 3.58500 2.95900
> Why does it say there are no SOL molecules. Where exactly am I going wrong ?
> Kindly advice me. Thankyou for your patience.
> sharada
>
My guess would be that it is because there are no molecules named SOL in your
output. Gromacs uses SOL for water, and since your system lacks water, genbox
is accurately telling you there are no "SOL" within the output.
Note the line above where genbox is telling you that it added 522 molecules, and
add this information into your .top file.
-Justin
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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