Hi Dan,
I am calculating the RMSF value using the following script.
1. No matter I specify the residue numbers (1-416, which is only the
protein) or I don't specify the residue numbers. The output I got from
CPPTRAJ is weird, the residues 209 to 216 (also protein) are always
missing. Is the script correct?
2. If I want to perform an RMS fit to the first structure prior to the
calculation, is "rms first" the correct command?
3. Usually, fit to the average structure or the first structure?
Looking forward to your feedback, thank you.
parm all_stripWI.prmtop
trajin all_stripWI.nc
#rms first
atomicfluct out rmsf_bb_dimer_try.dat .C,CA,N byres
go
quit
Best regards,
Rui
On Wed, Oct 2, 2019 at 8:41 AM Rui Chen <rchen6.ualberta.ca> wrote:
> Hi Dan,
>
> We found a solution in the following link:
> http://archive.ambermd.org/201604/0469.html, which parmed gave someone
> the similar error.
> "fixatomorder outprefix reorder" command helped me solve the problem, the
> output trajectory was .nc (AMBER) format.
>
> Best regards,
> Rui
>
>
> On Wed, Oct 2, 2019 at 7:32 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Tue, Oct 1, 2019 at 6:36 PM Rui Chen <rchen6.ualberta.ca> wrote:
>> > I uploaded a parameter file into CPPTRAJ. I got the following errors. I
>> > double checked the atom numbering is sequential. It seems like the
>> problem
>>
>> It's not that atom numbering is sequential - it's that the atom range
>> in the molecule is not completely contiguous. So something like this:
>>
>> Molecule 1: Atoms 1 2 3 4 10 11 12 13
>> Molecule 2: Atoms 5 6 7 8 9
>>
>> Cpptraj (and I think other programs in Amber as well) operates on the
>> assumption that molecules are completely contiguous (this is
>> beneficial for a lot of reasons). When they aren't, cpptraj kicks back
>> this error. I think parmed will give you a similar warning.
>>
>> > Just to let you know, this is a homodimer and the following mentioned
>> atom
>> > 6615 is the first atom of the glycans. I think the problem is the
>> > glycan/protein interactions. I tried the four ways mentioned in the
>> first
>> > snapshot, none of them worked.
>>
>> Can you elaborate on *exactly* what you did and describe exactly why
>> it didn't work? We need way more information to help.
>>
>> -Dan
>>
>> >
>> > Could you please give me some clues? Looking forward to your reply.
>> >
>> > [image: Screen Shot 2019-10-01 at 3.45.59 PM.png]
>> >
>> > [image: Screen Shot 2019-10-01 at 3.47.01 PM.png]
>> >
>> > Best regards,
>> > Rui
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 02 2019 - 15:30:02 PDT
