Hi,
Thanks for the files.
So I'm not sure from what restart file you originally posted, but the
restart file you provided indeed has no box lengths:
$ tail cpx_trpc6_lig1234_vmd.rst7
189.0290070 191.1210022 79.3610001 188.1759949 191.1479950 79.8539963
188.8079987 191.7709961 78.6460037 190.8939972 190.2449951 81.1250000
190.2180023 190.6580048 80.5289993 191.4479980 189.8049927 80.4459991
191.0240021 189.3040009 78.3399963 191.5279999 189.6609955 77.5770035
190.3419952 189.9940033 78.4469986 194.8569946 188.6029968 81.9499969
194.8750000 189.5509949 82.1880035 194.8220062 188.2039948 82.8570023
192.5800018 190.2070007 76.1800003 193.1390076 189.5899963 75.6569977
193.2859955 190.7169952 76.6439972 197.0240021 192.2440033 78.1320038
197.4010010 191.6999969 78.8679962 196.9949951 193.1179962 78.5989990
0.0000000 0.0000000 0.0000000 90.0000000 90.0000000 90.0000000
If you're certain you know what the box lengths are supposed to be, you can
set them with cpptraj:
parm cpx_trpc6_lig1234.prmtop
trajin cpx_trpc6_lig1234_vmd.rst7
box x 190 y 190 z 190 alpha 90 beta 90 gamma 90
trajout box.cpx_trpc6_lig1234_vmd.rst7
However, it's probably worth trying to figure out how you lost your box
info in the first place. I used the 'check' action in cpptraj to check your
system using the box lengths you specified and I got over 5000 warnings
about close contacts - how did you generate the system in the first place?
-Dan
On Thu, Oct 26, 2023 at 9:22 PM Xavier Wezen Chee <XChee.swinburne.edu.my>
wrote:
> Dear Dan, thanks for the prompt response.
> It seems that the box vector length is not found.
> But i would have presume that the last line of the rst7 (190.0000000
> 190.0000000 190.0000000 90.0000000 90.0000000 90.0000000) would be the box
> length?
>
> Thanks for your help, Dan. Pls find the files as attached.
> cpx_trpc6_lig1234.prmtop
> <https://swinburnesarawak-my.sharepoint.com/:u:/g/personal/xchee_swinburne_edu_my/EQCr1q-fYqhErSR2pLQSeZ0BhZnL_4755OqfOusDra268A>
> cpx_trpc6_lig1234_vmd.rst7
> <https://swinburnesarawak-my.sharepoint.com/:u:/g/personal/xchee_swinburne_edu_my/ET7AMXuaIuVCvp_wtcbKRvcBJzZOJ8m6ddHFCedMoawKQw>
>
>
> Output from the command *cpptraj -p cpx_trpc6_lig1234.prmtop -y
> cpx_trpc6_lig1234_vmd.rst7 -x test.pdb*
>
> CPPTRAJ: Trajectory Analysis. V6.4.4 (AmberTools) OpenMP
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | 1 OpenMP threads available.
> | Date/time: 10/27/23 11:54:51
> | Available memory: 129.949 GB
>
> Reading 'cpx_trpc6_lig1234.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> Reading 'cpx_trpc6_lig1234_vmd.rst7' as Amber Restart
> Warning: Box X vector length is zero.
> Warning: Box Y vector length is zero.
> Warning: Box Z vector length is zero.
> Writing 'test.pdb' as PDB
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: cpx_trpc6_lig1234.prmtop, 792246 atoms, 208430 res, box: None, 203090
> mol, 200926 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: 'cpx_trpc6_lig1234_vmd.rst7' is an AMBER restart file, no velocities,
> Parm cpx_trpc6_lig1234.prmtop (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> OUTPUT TRAJECTORIES (1 total):
> 'test.pdb' (1 frames) is a PDB file
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTIVE OUTPUT TRAJECTORIES (1):
> test.pdb (coordinates)
> ----- cpx_trpc6_lig1234_vmd.rst7 (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
> TIME: Avg. throughput= 0.6984 frames / second.
>
> ACTION OUTPUT:
> TIME: Analyses took 0.0000 seconds.
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 0.00%)
> TIME: Trajectory Process : 1.4319 s ( 99.98%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0000 s ( 0.00%)
> TIME: Other : 0.0003 s ( 0.00%)
> TIME: Run Total 1.4323 s
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 2.1928 seconds.
>
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
> ------------------------------
> *From:* Daniel Roe <daniel.r.roe.gmail.com>
> *Sent:* Friday, October 27, 2023 8:28 AM
> *To:* Xavier Wezen Chee <XChee.swinburne.edu.my>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE
>
> Hi,
>
> Try to convert it to a different format with cpptraj; it may be able
> to give you a different error message that might provide a clue to
> what could be going on.
>
> cpptraj -p <topology file> -y <restart file> -x test.mol2
>
> If that doesn't provide anything useful, send me the topology and
> restart off-list and I'll look at it.
>
> -Dan
>
> On Thu, Oct 26, 2023 at 6:46 PM Xavier Wezen Chee via AMBER
> <amber.ambermd.org> wrote:
> >
> > Dear all, I am getting this error message but i am not entirely sure why
> and how to fix it.
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> > peek_ewald_inpcrd: SHOULD NOT BE HERE
> > 190.0000 190.0000 190.0000 90.0000 90.0000 90.0000
> >
> > This is the last few lines of the rst7 file
> > 189.0290070 191.1210022 79.3610001 188.1759949 191.1479950 79.8539963
> > 188.8079987 191.7709961 78.6460037 190.8939972 190.2449951 81.1250000
> > 190.2180023 190.6580048 80.5289993 191.4479980 189.8049927 80.4459991
> > 191.0240021 189.3040009 78.3399963 191.5279999 189.6609955 77.5770035
> > 190.3419952 189.9940033 78.4469986 194.8569946 188.6029968 81.9499969
> > 194.8750000 189.5509949 82.1880035 194.8220062 188.2039948 82.8570023
> > 192.5800018 190.2070007 76.1800003 193.1390076 189.5899963 75.6569977
> > 193.2859955 190.7169952 76.6439972 197.0240021 192.2440033 78.1320038
> > 197.4010010 191.6999969 78.8679962 196.9949951 193.1179962 78.5989990
> > 190.0000000 190.0000000 190.0000000 90.0000000 90.0000000 90.0000000
> >
> > And i've checked that there are no empty lines after rst7.
> > Any advice would be appreciated. Thanks!
> >
> > Regards,
> > Xavier Chee
> >
> >
> > [cid:8d84cebd-8266-44cb-9817-57ebcb153567]
> >
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Received on Fri Oct 27 2023 - 10:30:01 PDT
