MODELLER and external constraints (such as NMR)
Dear MODELLER users:
I wonder whether anyone have tried to incoporate external constraints such as those from NMR in modeling.
I have some NMR constraints derived from NOE and want to incorporate them into molecular dynamics step, but have no idea how to get start, such as the format (page 72 manual) and the command in TOP file. By the way, I have got the model using "fully automated comparative modeling."
Thanks for any comments.
Best regards,
Chunhua Yuan
Hi,
please look at the ADD_RESTRAINTS command. With that one you can add your NMR distance restraints or any kind of the 31 available other restraint types. The parameter format is discussed in the manual "Specification of restraints" in 2.5. Examples are given in the command discussion of ADD_restraints. Also please look at Freq. Asked question in the manual: example 8,9,10,11.
best wishes
Andras
chunhua yuan wrote: > > Dear MODELLER users: > > I wonder whether anyone have tried to incoporate external > constraints such as those from NMR in modeling. > > I have some NMR constraints derived from NOE and want to > incorporate them into molecular dynamics step, but have no idea how to > get start, such as the format (page 72 manual) and the command in TOP > file. By the way, I have got the model using "fully automated > comparative modeling." > > Thanks for any comments. > > Best regards, > > Chunhua Yuan
Dear Andras:
Many thanks for your help. After I got your message, I spent these two days to understand the manual and examples that you pointed out. I followed Examples 9 and 10 (page 106-107, manual) to take a test, but have not succeeded yet. The following are my new questions:
(1) Variable name not recognized: RESTRAINED_ATOMS in example 10.
(2) Variable name not recognized: ALIGNMENT_FILE, but it works with "ALNFILE".
(3) The log file of example 9 gave a error message "rdcsr1___E> wrong key: ".
(4) Does examples 9 use both homology-derived restraints and user-added constraints in modeling? I have a hard time to understand that "ADD_restraints" is "off"(page 84, manual). If yes, what is the difference between example 9 and 10? in the restraint file?
(5) What is the difference between Group 28 and Group 29 on page 74? both are NMR distance constraints.
(6) NOE-derived distance constraints are usually specified in terms of a distance range, what is the best form for thse constraints in MODELLER (page 73, manual)?
(7) Equation (6.59) on page 129 could have typo in conditions.
(8) If external constraints contradict with the homology-derived constraints, what will happen and what should we do?
I am sorry to give you a long list of questions. I would greatly appreciate your help.
! ! ! !
Best regards,
Chunhua Yuan
Andras Fiser wrote: > > Hi, > > please look at the ADD_RESTRAINTS command. With that one you can add your NMR > distance restraints or any kind of the 31 available other restraint types. The > parameter format is discussed in the manual "Specification of restraints" in > 2.5. Examples are given in the command discussion of ADD_restraints. Also > please look at Freq. Asked question in the manual: example 8,9,10,11. > > best wishes > > Andras >
Hi Chunhua,
> followed Examples 9 and 10 (page 106-107, manual) to take a test, but > have not succeeded yet. The following are my new questions: > > (1) Variable name not recognized: RESTRAINED_ATOMS in example 10.
following your example, please replace your line in file p15_test2:
SET RESTRAINED_ATOMS = 'CA' 'CA', RESIDUE_IDS = '2' '10'
with
set ATOM_IDS = 'CA:2' 'CA:10'
for me it works now.
Your other top file, which reads the restraints, directly from a file, looks as if it is OK. You did not write any problem, I hope it works for you as well.
> (2) Variable name not recognized: ALIGNMENT_FILE, but it works with > "ALNFILE". > > (3) The log file of example 9 gave a error message "rdcsr1___E> > wrong key: ". > > (4) Does examples 9 use both homology-derived restraints and > user-added constraints in modeling? I have a hard time to understand > that "ADD_restraints" is "off"(page 84, manual). If yes, what is the > difference between example 9 and 10? in the restraint file?
ADD_retsraints =off means everything is to be deleted whatever was before, and use the new, actually read restraints (in this case -example 9 - this is the default CSRFILE). When you read the my-rsr1.rsr than you set ADD_RESTRAINTS= on, because you wish to keep the CSRFILE >and< add this new one. etc.
MODELLER automaticly derives angle, dih angle, distance etc etc restraints during its run, which by default are used during the optimization.
You have several choices: you can say, that you do not need any of the automaticly derived restraints, because you want to use only your own restraints: example 11.
In your case there is an other situation (if I am correct): you wish to keep the automaticly derived restraints and add your new ones from NMR experiments. You can do it in two ways: If you have only a few one you can include them in the top file (example 10) or if you have let's say a few hundred than it is better to create and read in the new , additional restrains from a file or from files. (example 9)
> (5) What is the difference between Group 28 and Group 29 on page > 74? both are NMR distance constraints.
Basicly nothing, this is only to document your restraint file: there is no difference if you choose any of them even if you choose 1 or 27 etc. But it is a good idea to annotate your new restraints corrdctly, e.g. as 28 or 29 because than they will be listed in that row in the restraints table that is reported in the log file. So you can see the summary of your restraints,as a fast check, if they are included or not.
> (6) NOE-derived distance constraints are usually specified in terms > of a distance range, what is the best form for thse constraints in > MODELLER (page 73, manual)?
Probably the best in case of NOE to define an upper limit ( form 2 page 74) because that is what you usually know from NOE.
> (7) Equation (6.59) on page 129 could have typo in conditions.
well, It looks to me that the third condition may be incorrect , we will check it.
> (8) If external constraints contradict with the homology-derived > constraints, what will happen and what should we do?
Modeller will try to optimise all the restraints simultaneously. In the Log file you will see the violated restraints if you see serious contradiction it is better to remove some of the restrains.
When Modeller5 is released, probably there will be a more up-to-date manual as well.
I send this message for modeller_user group as well.
Best wishes
Andras
participants (2)
-
Andras Fiser -
chunhua yuan