计算化学公社

标题: 关于计算RMSD时报错，提示需要3或6个数值，现在只有1个 [打印本页]

作者
Author: 我要吃泡面 时间: 2024-6-26 17:14
标题: 关于计算RMSD时报错，提示需要3或6个数值，现在只有1个
Error: In gamd2.trj, expect only 3 or 6 box coords, got 1
Error: Box line=[ 46.112
]
Error: Could not set up 'gamd2.trj' for reading.
Error: Could not set up input trajectory 'gamd2.trj'.
(, 下载次数 Times of downloads: 1)

作者
Author: student0618 时间: 2024-6-26 17:51
本帖最后由 student0618 于 2024-6-26 18:12 编辑

What is the command you use? What is the input file you use?

I guess you are running analysis in CPPTRAJ, that it has problem when reading the trajectory. If so what is the command you are trying to run? What is the format of your trajectory?

作者
Author: 我要吃泡面 时间: 2024-6-27 08:52

student0618 发表于 2024-6-26 17:51
What is the command you use? What is the input file you use?

I guess you are running analysis in ...

Thank you for your answer, my command is
parm ../wt_dry.prmtop
trajin gamd2.trj 1 40000
but the file is so big that I cannot upload, maybe I can send you a mail.

作者
Author: student0618 时间: 2024-6-27 11:44
本帖最后由 student0618 于 2024-6-27 11:52 编辑

What is the format of your trajectory? Amber support more than one. If your trajectory has no problem it's possible that cpptraj don't get the right format.

Check what trajectory format you output in MD. You may need to specify the format, or rename the gamd2.trj with a proper extension like gamd2.nc/gamd2.crd etc depends on the actual format.

作者
Author: 我要吃泡面 时间: 2024-6-27 12:15

student0618 发表于 2024-6-27 11:44
What is the format of your trajectory? Amber support more than one. If your trajectory has no proble ...

Thank you, the format is .trj, I will try to change the format.

作者
Author: student0618 时间: 2024-6-27 12:22
本帖最后由 student0618 于 2024-6-27 12:24 编辑

Amber itself produce either netcdf (nc) or crd trajectories.trj is not a format it recognize.

From Amber23 manual: input trajectory format supported by cpptraj
(, 下载次数 Times of downloads: 24)

作者
Author: 我要吃泡面 时间: 2024-6-28 10:55
Thank you for your answer, I have found the reason

欢迎光临计算化学公社 (http://bbs.keinsci.com/)