Hi Dan,
Sorry for the late reply. I am using "CPPTRAJ: Version V4.25.6
(AmberTools V20.13)". The output I get is pasted below.
It does not seem to give any warnings about corrupted trajectory, but it
states that 0 native contacts were set up...May this be the reason for
all the "-nan" entries?
Thank you and best regards,
Richard
CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.13)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 05/07/21 11:26:41
| Available memory: 116.255 GB
INPUT: Reading input from 'contact.1.1904.cpptraj'
[parm ../../remd/cpptrajfiles/topology-no_water.parm7]
Reading '../../remd/cpptrajfiles/topology-no_water.parm7' as Amber
Topology
Radius Set: modified Bondi radii (mbondi)
[trajin remd_combine.1904.1.nc]
Reading 'remd_combine.1904.1.nc' as Amber NetCDF
[nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
tri_1904.1.pdb]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1-500&!.H*' Mask2=':501-503&!.H*', native
contacts set up based on first frame.
Distance cutoff is 4.5 Angstroms, imaging is on.
Mask selection will not include solvent.
Data set name: Contacts_00001
Contact stats will be written to 'STDOUT'
Contact res pairs will be written to 'STDOUT'
Contact PDB will be written to 'tri_1904.1.pdb'
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: topology-no_water.parm7, 8058 atoms, 514 res, box: Trunc. Oct., 13 mol
INPUT TRAJECTORIES (1 total):
0: 'remd_combine.1904.1.nc' is a NetCDF AMBER trajectory with
coordinates, time, replicaDims, replica indices, coordinate indices,
box, 1 replica dimensions, Parm topology-no_water.parm7 (Trunc. Oct.
box) (reading 12933 of 12933)
Coordinate processing will occur on 12933 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'topology-no_water.parm7' (1 actions):
0: [nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
tri_1904.1.pdb]
Mask [:1-500&!.H*] corresponds to 4063 atoms.
Mask [:501-503&!.H*] corresponds to 33 atoms.
4063 potential contact sites for ':1-500&!.H*'
33 potential contact sites for ':501-503&!.H*'
Imaging enabled.
----- remd_combine.1904.1.nc (1-12933, 1) -----
Using first frame to determine native contacts.
Mask [:1-500&!.H*] corresponds to 4063 atoms.
Mask [:501-503&!.H*] corresponds to 33 atoms.
Setup 0 native contacts:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 12933 frames and processed 12933 frames.
TIME: Avg. throughput= 53.4853 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
Writing contacts PDB to 'tri_1904.1.pdb'
TIME: Analyses took 0.0000 seconds.
DATASETS (2 total):
Contacts_00001[native] "Contacts_00001[native]" (integer), size is
12933 (51.732 kB)
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer),
size is 12933 (51.732 kB)
Total data set memory usage is at least 103.464 kB
DATAFILES (3 total):
STDOUT (Native Contacts)
tri_1904.1.pdb (Contact PDB)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 241.8046 s ( 99.98%)
TIME: Action Post : 0.0371 s ( 0.02%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0001 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 241.8419 s
---------- RUN END ---------------------------------------------------
On 5/3/21 5:48 PM, Daniel Roe wrote:
> Hi,
>
> What version of cpptraj are you using? Are there any warnings in the output
> about possible corruption in the trajectory?
>
> -Dan
>
> On Mon, May 3, 2021 at 10:28 AM Richard Kullmann <
> Richard.Kullmann.mpikg.mpg.de> wrote:
>
>> Hi all,
>>
>> I am trying to determine the average number of contacts over a
>> trajectory between receptor (residue 1 to 500) and ligand (residue 501
>> to 503) and create a pdb with corresponding beta-factor. The script I
>> use is the following:
>>
>> parm ../../remd/cpptrajfiles/topology-no_water.parm7
>> trajin remd_combine.1904.1.nc
>> nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
>> tri_1904.1.pdb
>> run
>> quit
>>
>> This runs through, but in the end, all beta factors are just -nan.
>> What am I doing wrong or is what I am trying to do just not possible?
>>
>> Thanks a lot in advance for your help.
>>
>> Best regards,
>>
>> Richard
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon May 10 2021 - 07:00:03 PDT
