You could use and atomnamemap in leap.
Bill
On 10/13/17 10:10 AM, Eiros Zamora, Juan wrote:
> 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 - 14:00:02 PDT
