From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Wed Sep 08 2010 - 16:28:50 CDT
OK: I assumed that since you acknowledged that 2.7b1 was buggy, you were
using 2.7b2 now, which should work. If it still doesn't with 2.7b2, there
may be a mismatch with the topology, or some bug we don't know of.
What about trying the following in VMD?
[atomselect top "(segid A) and (resid 386 to 485)"] get serial
[atomselect top "(segid A) and (resid 628 to 673)"] get serial
.. (and similar ones for B, C, and D) ...
If the atom numbers you get are less than expected, then there is something
wrong with the topology. Otherwise, you should send to me and Jérôme the
files, so that we investigate the error. In the meantime, you can use the
numbers provided by those VMD commands as an argument to atomNumbers in
NAMD. Does that work for you?
Giacomo
---- ----
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu
---- ----
On Tue, Sep 7, 2010 at 4:31 PM, dhacademic <dhacademic_at_gmail.com> wrote:
> Actually I had tried different combinations in atom definition part. None
> of them work well.
>
> (1) "psfSegID A A B B C C D D" and then 8 instances of
> "atomNameResidueRange".
> (2) "psfSegID A A B B C C D D" and then 2 instances of
> "atomNameResidueRange".
> (3) 8 instances of "atomNameResidueRange" and then "psfSegID A A B B C C D
> D".
> (4) 2 instances of "atomNameResidueRange""psfSegID A A B B C C D D".
>
> If I just specify 2 instances of atomNameResidueRange, 236 atoms can be
> selected (that is the number of atoms on each segment). But when 8 instances
> of atomNameResidueRange is assigned, then 237 atoms will be defined. I do
> not know where does this additional atoms come from.
>
>
>
>
>
> On Tue, Sep 7, 2010 at 12:23 PM, Giacomo Fiorin <giacomo.fiorin_at_temple.edu
> > wrote:
>
>> Did you specify only two instances of atomNameResidueRange? If that's
>> case, no wonder that segments B, C and D were ignored.
>>
>>
>> Giacomo
>>
>> ---- ----
>> Dr. Giacomo Fiorin
>> ICMS - Institute for Computational Molecular Science - Temple University
>> 1900 N 12 th Street, Philadelphia, PA 19122
>> giacomo.fiorin_at_temple.edu
>> ---- ----
>>
>>
>>
>>
>
>> On Mon, Sep 6, 2010 at 6:26 PM, dhacademic <dhacademic_at_gmail.com> wrote:
>>
>>> Hi Jerome and Giacomo,
>>>
>>> I have tried the following syntax (in colvars.conf file) according to the
>>> reply:
>>> atoms {
>>>
>>> psfSegID A A B B C C D D
>>> atomNameResidueRange CA 386-485
>>> atomNameResidueRange CA 628-763
>>> }
>>> And I still meet a similar output shown as follow. This time 236 atoms on
>>> segment A can be selected. However, the rest atoms on segment B, C, D are
>>> still ignored. It looks like that this atom definition error comes from to
>>> the bug of the version 2.7b1.
>>>
>>> #### my output file ####
>>> ....
>>> colvars: Initializing atom group "atoms".
>>> colvars: Warning: found more than one instance of "psfSegID".
>>> colvars: Atom group "atoms" defined, 236 atoms, total mass =
>>> 2834.6.
>>>
>>> colvars: # refPositionsFile = colvarb.pdb
>>> colvars: # refPositionsCol = B
>>> colvars: # refPositionsColValue = 1
>>> colvars: Error: the PDB file "colvarb.pdb" contains coordinates for
>>> only 87342 atoms, but 236 are needed.
>>> .....
>>>
>>> Best,
>>>
>>> Hao
>>>
>>>
>>>
>>> On Mon, Sep 6, 2010 at 3:10 PM, Giacomo Fiorin <
>>> giacomo.fiorin_at_temple.edu> wrote:
>>>
>>>> It would be best to use 2.7b2 or 2.7b3, in general.
>>>>
>>>> In the specific example, you used four psfSegID values but you specified
>>>> them separately: the correct syntax is to put them on the same line (one
>>>> psfSegID keyword with multiple values).
>>>>
>>>> Also, there may be only one atomNameResidueRange option for each
>>>> psfSegID value, not two of them as in your case. You should use something
>>>> like "psfSegID A A B B C C D D" to fix this.
>>>>
>>>> Giacomo
>>>>
>>>>
>>>> ---- ----
>>>> Dr. Giacomo Fiorin
>>>> ICMS - Institute for Computational Molecular Science - Temple
>>>> University
>>>> 1900 N 12 th Street, Philadelphia, PA 19122
>>>> giacomo.fiorin_at_temple.edu
>>>> ---- ----
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, Sep 6, 2010 at 11:29 AM, dhacademic <dhacademic_at_gmail.com>wrote:
>>>>
>>>>> my version is NAMD 2.7b1
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Sep 6, 2010 at 11:14 AM, Jérôme Hénin <
>>>>> jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> First, for TMD, you probably need the restraint force, so you should
>>>>>> request outputAppliedForce, not outputSystemForce.
>>>>>>
>>>>>>
>>>>>> > (1) Do the "centers" and "targets" keywords mean the initial and
>>>>>> final RMSD
>>>>>> > of the system? I feel confused by reading the related part of the
>>>>>> > user-manual.
>>>>>>
>>>>>> They are the initial and final values of the center of the restraint
>>>>>> potential. If all goes well, the RMSD should follow.
>>>>>>
>>>>>>
>>>>>> > (2) I want to define 4 (segments) * 236 (per segment) = 944 atoms in
>>>>>> the
>>>>>> > input. However, only 237 atoms are defined according to the output
>>>>>> > file. Someone else used a similar way to define atoms within
>>>>>> different
>>>>>> > segments
>>>>>> > (
>>>>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12359.html)--001485ed5748e05b46048fc634ee--
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