From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 17 2016 - 14:56:01 CST
Take a look at the end of the psf file you sent. Its truncated midway through line 344. Your script to generate the psf looks solid, so I don't know how this happened. The truncation would be why solvate won't work on it. Did the psfgen script give you any errors? This is definitely weird, but might go away if you just rerun the generation script.
On 11/17/2016 01:47 PM, Nehad Elsalamouny wrote:
Thanks for your email. I got the rtf file from http://mackerell.umaryland.edu/charmm_ff.shtml, downloaded toppar_c36_jul16.tgz<http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul16.tgz> and used the parm14sb_all.rtf file in non-charmm folder.
Atomtypes are alphanumeric. Part of the psf file is attached. I don't know what is the problem!
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