On 04/23/2013 06:02 PM, David A Case wrote:
> On Tue, Apr 23, 2013, Jan-Philip Gehrcke wrote:
>>
>> Since both types work independently in pmemd, I guess only minor changes
>> are required to make the combination also work :-) To the developers: is
>> it hard to make the combination of both restraint types work in
>> pmemd(.cuda)?
>
> Is it true that you can't combine these? Can you make a simple test case?
> What is the error message?
>
While I was quite sure that I observed this problem in the past (pretty
sure also with Amber 12), I was not able to reproduce it in systematic
tests with a small protein. Rahull, which Amber version are you using?
Input file for my test cases:
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 300,
ntb = 1,
ntr = 1,
cut = 8.0,
ig = -1,
nmropt = 1,
restraint_wt = 10.0,
restraintmask = "!:WAT",
/
&wt type='END' /
DISANG=restraints.rest
LISTIN=POUT
LISTOUT=POUT
restraints.rest for torsional restraint, old syntax:
&rst
iat=675, 678, 681, 684,
r1=50, r2=60, r3=70, r4=80, rk2=10, rk3=10
&end
restraints.rest for torsional restraint, natural syntax:
&rst
restraint="torsion(:42.CB, :42.CG, :42.CD, :42.NE)",
r1=50, r2=60, r3=70, r4=80, rk2=10, rk3=10
&end
restraints.rest for distance restraint, old syntax:
&rst
iat=1312, 1857,
r1=10.6, r2=10.7, r3=10.7, r4=10.8, rk2=100, rk3=100
&end
restraints.rest for distance restraint, natural syntax:
&rst
restraint="distance(:82.CB, :115.CA)",
r1=10.6, r2=10.7, r3=10.7, r4=10.8, rk2=100, rk3=100
&end
Amber patch level:
$ ./patch_amber.py --patch-level
Latest patch applied to AmberTools12: 35
Latest patch applied to Amber12: 15
Test class I: minimization with positional restraints on entire solute
via ntr=1 and distance restraint via nmropt=1 & DISANG file
->
- sander, natural restraint syntax: success
- sander, old restraint syntax: success
- pmemd, natural restraint syntax: fail
- pmemd, old restraint syntax: success
- pmemd.cuda, natural restraint syntax: fail
- pmemd.cuda, old restraint syntax: success
Test class II: minimization with positional restraints on entire solute
via ntr=1 and torsional restraint via nmropt=1 & DISANG file
->
- sander, natural restraint syntax: success
- sander, old restraint syntax: success
- pmemd, natural restraint syntax: fail
- pmemd, old restraint syntax: success
- pmemd.cuda, natural restraint syntax: fail
- pmemd.cuda, old restraint syntax: success
I think this is as expected, right?
>
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Received on Wed Apr 24 2013 - 02:00:02 PDT
