Dear Amberists,
I have a PDB file which was written by NAMD and I am trying to use it to prepare a model to be run with AMBER.
I’ve put TER commands between the non bonded regions of the system, and when I pass it trough pdb4amber, no warnings come up:
$ pdb4amber -i first10k.pdb > first10k_4amber.pdb
==================================================
Summary of pdb4amber for: first10k.pdb
===================================================
----------Chains
The following (original) chains have been found:
A
B
D
---------- Alternate Locations (Original Residues!))
The following residues had alternate locations:
None
---------- Mising heavy atom(s)
None
The system does not have any non-standard aminoacids other than HIP and HIE histidines.
When I run it through tleap, though, I get the following errors:
source oldff/leaprc.ff14SB
pdb = loadpdb first10k_4amber.pdb
FATAL: Atom .R<NASP 1>.A<CAY 15> does not have a type.
FATAL: Atom .R<NASP 1>.A<CY 16> does not have a type.
FATAL: Atom .R<NASP 1>.A<OY 17> does not have a type.
FATAL: Atom .R<HIP 73>.A<CZ 19> does not have a type.
FATAL: Atom .R<CPHE 375>.A<OT1 22> does not have a type.
FATAL: Atom .R<CPHE 375>.A<OT2 23> does not have a type.
FATAL: Atom .R<NASP 376>.A<CAY 15> does not have a type.
FATAL: Atom .R<NASP 376>.A<CY 16> does not have a type.
FATAL: Atom .R<NASP 376>.A<OY 17> does not have a type.
FATAL: Atom .R<HIP 448>.A<CZ 19> does not have a type.
FATAL: Atom .R<CPHE 750>.A<OT1 22> does not have a type.
FATAL: Atom .R<CPHE 750>.A<OT2 23> does not have a type.
FATAL: Atom .R<NASP 751>.A<CAY 15> does not have a type.
FATAL: Atom .R<NASP 751>.A<CY 16> does not have a type.
FATAL: Atom .R<NASP 751>.A<OY 17> does not have a type.
FATAL: Atom .R<HIP 823>.A<CZ 19> does not have a type.
FATAL: Atom .R<CPHE 1125>.A<OT1 22> does not have a type.
FATAL: Atom .R<CPHE 1125>.A<OT2 23> does not have a type.
Shouldn't pdb4amber complain about the atom names that don’t have a type in the ff14SB force field?
Does anyone have a suggestion on how can I convert the atom names in NAMD to AMBER? I’ve found a couple of online tools (
http://feig.bch.msu.edu/mmtsb/Convpdb.pl and
http://thegrantlab.org/bio3d/html/convert.pdb.html ) but neither change the problematic atom names.
[Sorry if this email appears twice, I had uploaded the logs but they’re too big and got bounced. I *think* I cancelled the message, if you want the logs and PDB I can send them privately]
Best regards,
Juan
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Received on Fri Oct 13 2017 - 10:30:02 PDT
