Thank you for quick reply.
The wat_pack.pdb contain only repeating water molecule and "WAT" is residue
name.`
ATOM 1 O WAT A 1 9.649 18.830 4.849 1.00 0.00
ATOM 2 H1 WAT A 1 10.382 19.458 4.852 1.00 0.00
ATOM 3 H2 WAT A 1 9.994 18.025 4.443 1.00 0.00
TER
Thank you
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
On Thu, Mar 27, 2014 at 1:16 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Mar 26, 2014, MOHD HOMAIDUR RAHMAN wrote:
>
> > source leaprc.ff99bsc0
> > WAT = SPC
> > HOH = SPC
> > loadAmberParms frcmod.spce
> > set SPC.1 name "SPC"
>
> Why did you do this? It might well have some undesirable side-effects;
> waters
> are conventionally named WAT or HOH.
>
> > set default FlexibleWater on
>
> This is probably pretty bad: SPC/E is a rigid water model, not a flexible
> one.
>
> > RM = loadpdb wat_pack.pdb
>
> What are the residue names in the wat_pack.pdb file?
>
> > By searching SPC/E water model parameter in topology file, I found that
> the
> > leap taken the default TIP3P water model parameter.
>
> I don't immediately see why this would be happening; the one big unknown
> here
> is the contents of your pdb-file, so let's rule out problems there first.
>
> (Maybe some other eagle-eyed person on the list will spot the problem
> first)
>
> ...dac
>
>
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Received on Wed Mar 26 2014 - 22:30:02 PDT
